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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: X-103787829-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=103787829&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 103787829,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000621218.5",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLP1",
"gene_hgnc_id": 9086,
"hgvs_c": "c.485T>C",
"hgvs_p": "p.Val162Ala",
"transcript": "NM_000533.5",
"protein_id": "NP_000524.3",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 277,
"cds_start": 485,
"cds_end": null,
"cds_length": 834,
"cdna_start": 641,
"cdna_end": null,
"cdna_length": 3011,
"mane_select": "ENST00000621218.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLP1",
"gene_hgnc_id": 9086,
"hgvs_c": "c.485T>C",
"hgvs_p": "p.Val162Ala",
"transcript": "ENST00000621218.5",
"protein_id": "ENSP00000484450.1",
"transcript_support_level": 1,
"aa_start": 162,
"aa_end": null,
"aa_length": 277,
"cds_start": 485,
"cds_end": null,
"cds_length": 834,
"cdna_start": 641,
"cdna_end": null,
"cdna_length": 3011,
"mane_select": "NM_000533.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLP1",
"gene_hgnc_id": 9086,
"hgvs_c": "c.380T>C",
"hgvs_p": "p.Val127Ala",
"transcript": "ENST00000619236.1",
"protein_id": "ENSP00000477619.1",
"transcript_support_level": 1,
"aa_start": 127,
"aa_end": null,
"aa_length": 242,
"cds_start": 380,
"cds_end": null,
"cds_length": 729,
"cdna_start": 526,
"cdna_end": null,
"cdna_length": 2896,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLP1",
"gene_hgnc_id": 9086,
"hgvs_c": "c.485T>C",
"hgvs_p": "p.Val162Ala",
"transcript": "NM_001128834.3",
"protein_id": "NP_001122306.1",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 277,
"cds_start": 485,
"cds_end": null,
"cds_length": 834,
"cdna_start": 770,
"cdna_end": null,
"cdna_length": 3140,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLP1",
"gene_hgnc_id": 9086,
"hgvs_c": "c.485T>C",
"hgvs_p": "p.Val162Ala",
"transcript": "ENST00000612423.4",
"protein_id": "ENSP00000481006.1",
"transcript_support_level": 2,
"aa_start": 162,
"aa_end": null,
"aa_length": 277,
"cds_start": 485,
"cds_end": null,
"cds_length": 834,
"cdna_start": 765,
"cdna_end": null,
"cdna_length": 3132,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLP1",
"gene_hgnc_id": 9086,
"hgvs_c": "c.380T>C",
"hgvs_p": "p.Val127Ala",
"transcript": "NM_199478.3",
"protein_id": "NP_955772.1",
"transcript_support_level": null,
"aa_start": 127,
"aa_end": null,
"aa_length": 242,
"cds_start": 380,
"cds_end": null,
"cds_length": 729,
"cdna_start": 536,
"cdna_end": null,
"cdna_length": 2906,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLP1",
"gene_hgnc_id": 9086,
"hgvs_c": "c.320T>C",
"hgvs_p": "p.Val107Ala",
"transcript": "NM_001305004.1",
"protein_id": "NP_001291933.1",
"transcript_support_level": null,
"aa_start": 107,
"aa_end": null,
"aa_length": 222,
"cds_start": 320,
"cds_end": null,
"cds_length": 669,
"cdna_start": 463,
"cdna_end": null,
"cdna_length": 2833,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLP1",
"gene_hgnc_id": 9086,
"hgvs_c": "n.296T>C",
"hgvs_p": null,
"transcript": "ENST00000461231.5",
"protein_id": null,
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 560,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLP1",
"gene_hgnc_id": 9086,
"hgvs_c": "n.321T>C",
"hgvs_p": null,
"transcript": "ENST00000466486.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 861,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLP1",
"gene_hgnc_id": 9086,
"hgvs_c": "n.466T>C",
"hgvs_p": null,
"transcript": "ENST00000478642.5",
"protein_id": null,
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 627,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLP1",
"gene_hgnc_id": 9086,
"hgvs_c": "n.531T>C",
"hgvs_p": null,
"transcript": "ENST00000479569.5",
"protein_id": null,
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 671,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLP1",
"gene_hgnc_id": 9086,
"hgvs_c": "n.222T>C",
"hgvs_p": null,
"transcript": "ENST00000485688.5",
"protein_id": null,
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 566,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLP1",
"gene_hgnc_id": 9086,
"hgvs_c": "n.31T>C",
"hgvs_p": null,
"transcript": "ENST00000494119.1",
"protein_id": null,
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 566,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 8,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "ENSG00000288597",
"gene_hgnc_id": null,
"hgvs_c": "n.800+4852A>G",
"hgvs_p": null,
"transcript": "ENST00000674162.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
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"cdna_start": null,
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"cdna_length": 4248,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 7,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "ENSG00000288597",
"gene_hgnc_id": null,
"hgvs_c": "n.1490+3425A>G",
"hgvs_p": null,
"transcript": "ENST00000674193.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1746,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "ENSG00000288597",
"gene_hgnc_id": null,
"hgvs_c": "n.422+4852A>G",
"hgvs_p": null,
"transcript": "ENST00000674212.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
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"cdna_start": null,
"cdna_end": null,
"cdna_length": 2931,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "ENSG00000288597",
"gene_hgnc_id": null,
"hgvs_c": "n.736+4852A>G",
"hgvs_p": null,
"transcript": "ENST00000674236.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3285,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"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": "ENSG00000288597",
"gene_hgnc_id": null,
"hgvs_c": "n.246+4852A>G",
"hgvs_p": null,
"transcript": "ENST00000674255.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 553,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 7,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "ENSG00000288597",
"gene_hgnc_id": null,
"hgvs_c": "n.705+4852A>G",
"hgvs_p": null,
"transcript": "ENST00000674265.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
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"aa_length": null,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 994,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 10,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "ENSG00000288597",
"gene_hgnc_id": null,
"hgvs_c": "n.694+4852A>G",
"hgvs_p": null,
"transcript": "ENST00000674271.1",
"protein_id": null,
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"aa_start": null,
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"cds_start": -4,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "ENSG00000288597",
"gene_hgnc_id": null,
"hgvs_c": "n.768+4852A>G",
"hgvs_p": null,
"transcript": "ENST00000674274.1",
"protein_id": null,
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"aa_start": null,
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"aa_length": null,
"cds_start": -4,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ENSG00000288597",
"gene_hgnc_id": null,
"hgvs_c": "n.217+4852A>G",
"hgvs_p": null,
"transcript": "ENST00000674292.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 304,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 16,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "ENSG00000288597",
"gene_hgnc_id": null,
"hgvs_c": "n.408+4852A>G",
"hgvs_p": null,
"transcript": "ENST00000674338.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2745,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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},
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},
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}
],
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"dbsnp": "rs1556268920",
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"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.4096708297729492,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.429,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.2021,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.31,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.663,
"phylop100way_prediction": "Uncertain_significance",
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM1,PM2,PP2,BP4",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 1,
"pathogenic_score": 5,
"criteria": [
"PM1",
"PM2",
"PP2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000621218.5",
"gene_symbol": "PLP1",
"hgnc_id": 9086,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.485T>C",
"hgvs_p": "p.Val162Ala"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NR_146558.2",
"gene_symbol": "RAB9B",
"hgnc_id": 14090,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.432+4852A>G",
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},
{
"score": 1,
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"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000674162.1",
"gene_symbol": "ENSG00000288597",
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"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.800+4852A>G",
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}
],
"clinvar_disease": "Hereditary spastic paraplegia 2",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Hereditary spastic paraplegia 2",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}