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GeneBe API Showcase

This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.

API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.

Documentation & Advanced Usage

Complete API documentation:docs.genebe.net/docs/api/overview/

Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/

Python client for pandas:pypi.org/project/genebe/

Java CLI for VCF files:github.com/pstawinski/genebe-cli

All tools documented at:docs.genebe.net

API Request Examples for Variant: 19-49928131-G-A (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=49928131&ref=G&alt=A&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "19",
      "pos": 49928131,
      "ref": "G",
      "alt": "A",
      "effect": "intron_variant",
      "transcript": "NM_172374.3",
      "consequences": [
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "NUP62",
          "gene_hgnc_id": 8066,
          "hgvs_c": "c.-199-316C>T",
          "hgvs_p": null,
          "transcript": "NM_016553.5",
          "protein_id": "NP_057637.2",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 522,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1569,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "ENST00000352066.8",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_016553.5"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "NUP62",
          "gene_hgnc_id": 8066,
          "hgvs_c": "c.-199-316C>T",
          "hgvs_p": null,
          "transcript": "ENST00000352066.8",
          "protein_id": "ENSP00000305503.3",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 522,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1569,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "NM_016553.5",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000352066.8"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "IL4I1",
          "gene_hgnc_id": 19094,
          "hgvs_c": "c.-349-316C>T",
          "hgvs_p": null,
          "transcript": "ENST00000341114.7",
          "protein_id": "ENSP00000342557.2",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 589,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1770,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000341114.7"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "IL4I1",
          "gene_hgnc_id": 19094,
          "hgvs_c": "c.-407-316C>T",
          "hgvs_p": null,
          "transcript": "ENST00000595948.5",
          "protein_id": "ENSP00000472474.1",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 589,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1770,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000595948.5"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 2,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "NUP62",
          "gene_hgnc_id": 8066,
          "hgvs_c": "c.-78+1195C>T",
          "hgvs_p": null,
          "transcript": "ENST00000422090.2",
          "protein_id": "ENSP00000407331.1",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 522,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1569,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000422090.2"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "NUP62",
          "gene_hgnc_id": 8066,
          "hgvs_c": "c.-232-283C>T",
          "hgvs_p": null,
          "transcript": "ENST00000597029.6",
          "protein_id": "ENSP00000473192.1",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 522,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1569,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000597029.6"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 4,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "NUP62",
          "gene_hgnc_id": 8066,
          "hgvs_c": "c.-199-316C>T",
          "hgvs_p": null,
          "transcript": "ENST00000597723.5",
          "protein_id": "ENSP00000469283.1",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 446,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1341,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000597723.5"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": true,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": 2,
          "intron_rank_end": null,
          "gene_symbol": "ENSG00000269179",
          "gene_hgnc_id": null,
          "hgvs_c": "n.*78-18247C>T",
          "hgvs_p": null,
          "transcript": "ENST00000451973.1",
          "protein_id": "ENSP00000391489.1",
          "transcript_support_level": 2,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": null,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "nonsense_mediated_decay",
          "feature": "ENST00000451973.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "IL4I1",
          "gene_hgnc_id": 19094,
          "hgvs_c": "n.-349-316C>T",
          "hgvs_p": null,
          "transcript": "ENST00000601717.5",
          "protein_id": "ENSP00000469467.1",
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": null,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "nonsense_mediated_decay",
          "feature": "ENST00000601717.5"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "5_prime_UTR_premature_start_codon_gain_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 2,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "NUP62",
          "gene_hgnc_id": 8066,
          "hgvs_c": "c.-515C>T",
          "hgvs_p": null,
          "transcript": "ENST00000596217.1",
          "protein_id": "ENSP00000471191.1",
          "transcript_support_level": 2,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 522,
          "cds_start": null,
          "cds_end": null,
          "cds_length": 1569,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000596217.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "5_prime_UTR_premature_start_codon_gain_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "NUP62",
          "gene_hgnc_id": 8066,
          "hgvs_c": "c.-629C>T",
          "hgvs_p": null,
          "transcript": "ENST00000950749.1",
          "protein_id": "ENSP00000620808.1",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 522,
          "cds_start": null,
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          "cds_length": 1569,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000950749.1"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
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          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "NUP62",
          "gene_hgnc_id": 8066,
          "hgvs_c": "c.-777C>T",
          "hgvs_p": null,
          "transcript": "ENST00000950750.1",
          "protein_id": "ENSP00000620809.1",
          "transcript_support_level": null,
          "aa_start": null,
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          "aa_length": 522,
          "cds_start": null,
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          "cds_length": 1569,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
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        },
        {
          "aa_ref": null,
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          "protein_coding": true,
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          "consequences": [
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          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 2,
          "intron_rank": null,
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          "gene_symbol": "NUP62",
          "gene_hgnc_id": 8066,
          "hgvs_c": "c.-515C>T",
          "hgvs_p": null,
          "transcript": "ENST00000596217.1",
          "protein_id": "ENSP00000471191.1",
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          "cds_start": null,
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          "cdna_start": null,
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          "biotype": "protein_coding",
          "feature": "ENST00000596217.1"
        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
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          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 3,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "NUP62",
          "gene_hgnc_id": 8066,
          "hgvs_c": "c.-629C>T",
          "hgvs_p": null,
          "transcript": "ENST00000950749.1",
          "protein_id": "ENSP00000620808.1",
          "transcript_support_level": null,
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          "cds_start": null,
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          "mane_select": null,
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        },
        {
          "aa_ref": null,
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          ],
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          "intron_rank": null,
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          "gene_symbol": "NUP62",
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          "hgvs_c": "c.-777C>T",
          "hgvs_p": null,
          "transcript": "ENST00000950750.1",
          "protein_id": "ENSP00000620809.1",
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          "biotype": "protein_coding",
          "feature": "ENST00000950750.1"
        },
        {
          "aa_ref": null,
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          "canonical": false,
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          "strand": false,
          "consequences": [
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          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 10,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "IL4I1",
          "gene_hgnc_id": 19094,
          "hgvs_c": "c.-349-316C>T",
          "hgvs_p": null,
          "transcript": "NM_001258017.2",
          "protein_id": "NP_001244946.1",
          "transcript_support_level": null,
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          "cds_start": null,
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          "cdna_start": null,
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          "biotype": "protein_coding",
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        },
        {
          "aa_ref": null,
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          "canonical": false,
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          "consequences": [
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          ],
          "exon_rank": null,
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          "exon_count": 10,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "IL4I1",
          "gene_hgnc_id": 19094,
          "hgvs_c": "c.-407-316C>T",
          "hgvs_p": null,
          "transcript": "NM_001258018.2",
          "protein_id": "NP_001244947.1",
          "transcript_support_level": null,
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        },
        {
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          ],
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          "gene_symbol": "IL4I1",
          "gene_hgnc_id": 19094,
          "hgvs_c": "c.-349-316C>T",
          "hgvs_p": null,
          "transcript": "NM_172374.3",
          "protein_id": "NP_758962.1",
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        },
        {
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          "protein_coding": true,
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          ],
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          "gene_symbol": "NUP62",
          "gene_hgnc_id": 8066,
          "hgvs_c": "c.-78+1286C>T",
          "hgvs_p": null,
          "transcript": "NM_001193357.2",
          "protein_id": "NP_001180286.1",
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          "biotype": "protein_coding",
          "feature": "NM_001193357.2"
        },
        {
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          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
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          "exon_count": 2,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "NUP62",
          "gene_hgnc_id": 8066,
          "hgvs_c": "c.-78+1219C>T",
          "hgvs_p": null,
          "transcript": "NM_012346.5",
          "protein_id": "NP_036478.2",
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": 522,
          "cds_start": null,
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          "cds_length": 1569,
          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
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          "biotype": "protein_coding",
          "feature": "NM_012346.5"
        },
        {
          "aa_ref": null,
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          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
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          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 11,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "IL4I1",
          "gene_hgnc_id": 19094,
          "hgvs_c": "n.180-316C>T",
          "hgvs_p": null,
          "transcript": "NR_047577.2",
          "protein_id": null,
          "transcript_support_level": null,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": null,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "pseudogene",
          "feature": "NR_047577.2"
        }
      ],
      "gene_symbol": "IL4I1",
      "gene_hgnc_id": 19094,
      "dbsnp": "rs3826777",
      "frequency_reference_population": 0.3407107,
      "hom_count_reference_population": 9190,
      "allele_count_reference_population": 51833,
      "gnomad_exomes_af": 0.271429,
      "gnomad_genomes_af": 0.340743,
      "gnomad_exomes_ac": 19,
      "gnomad_genomes_ac": 51814,
      "gnomad_exomes_homalt": 2,
      "gnomad_genomes_homalt": 9188,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": -0.8799999952316284,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "BayesDel_noAF",
      "splice_score_selected": 0,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
      "revel_score": null,
      "revel_prediction": null,
      "alphamissense_score": null,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.88,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": -0.2,
      "phylop100way_prediction": "Benign",
      "spliceai_max_score": 0,
      "spliceai_max_prediction": "Benign",
      "dbscsnv_ada_score": null,
      "dbscsnv_ada_prediction": null,
      "apogee2_score": null,
      "apogee2_prediction": null,
      "mitotip_score": null,
      "mitotip_prediction": null,
      "acmg_score": -12,
      "acmg_classification": "Benign",
      "acmg_criteria": "BP4_Strong,BA1",
      "acmg_by_gene": [
        {
          "score": -12,
          "benign_score": 12,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BA1"
          ],
          "verdict": "Benign",
          "transcript": "NM_172374.3",
          "gene_symbol": "IL4I1",
          "hgnc_id": 19094,
          "effects": [
            "intron_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.-349-316C>T",
          "hgvs_p": null
        },
        {
          "score": -12,
          "benign_score": 12,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BA1"
          ],
          "verdict": "Benign",
          "transcript": "NM_012346.5",
          "gene_symbol": "NUP62",
          "hgnc_id": 8066,
          "effects": [
            "intron_variant"
          ],
          "inheritance_mode": "AR,AD,Unknown",
          "hgvs_c": "c.-78+1219C>T",
          "hgvs_p": null
        },
        {
          "score": -12,
          "benign_score": 12,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BA1"
          ],
          "verdict": "Benign",
          "transcript": "ENST00000451973.1",
          "gene_symbol": "ENSG00000269179",
          "hgnc_id": null,
          "effects": [
            "intron_variant"
          ],
          "inheritance_mode": "",
          "hgvs_c": "n.*78-18247C>T",
          "hgvs_p": null
        },
        {
          "score": -12,
          "benign_score": 12,
          "pathogenic_score": 0,
          "criteria": [
            "BP4_Strong",
            "BA1"
          ],
          "verdict": "Benign",
          "transcript": "ENST00000858032.1",
          "gene_symbol": "ATF5",
          "hgnc_id": 790,
          "effects": [
            "intron_variant"
          ],
          "inheritance_mode": "AR",
          "hgvs_c": "c.-277-1112G>A",
          "hgvs_p": null
        }
      ],
      "clinvar_disease": "",
      "clinvar_classification": "",
      "clinvar_review_status": "",
      "clinvar_submissions_summary": "",
      "phenotype_combined": null,
      "pathogenicity_classification_combined": null,
      "custom_annotations": null
    }
  ],
  "message": null
}