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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: 2-219157495-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=219157495&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 219157495,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_001377499.1",
"consequences": [
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NHEJ1",
"gene_hgnc_id": 25737,
"hgvs_c": "c.367T>C",
"hgvs_p": "p.Cys123Arg",
"transcript": "NM_024782.3",
"protein_id": "NP_079058.1",
"transcript_support_level": null,
"aa_start": 123,
"aa_end": null,
"aa_length": 299,
"cds_start": 367,
"cds_end": null,
"cds_length": 900,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000356853.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_024782.3"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NHEJ1",
"gene_hgnc_id": 25737,
"hgvs_c": "c.367T>C",
"hgvs_p": "p.Cys123Arg",
"transcript": "ENST00000356853.10",
"protein_id": "ENSP00000349313.5",
"transcript_support_level": 1,
"aa_start": 123,
"aa_end": null,
"aa_length": 299,
"cds_start": 367,
"cds_end": null,
"cds_length": 900,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_024782.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000356853.10"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000280537",
"gene_hgnc_id": null,
"hgvs_c": "n.*1489T>C",
"hgvs_p": null,
"transcript": "ENST00000318673.6",
"protein_id": "ENSP00000320919.3",
"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": "ENST00000318673.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000280537",
"gene_hgnc_id": null,
"hgvs_c": "n.*1489T>C",
"hgvs_p": null,
"transcript": "ENST00000318673.6",
"protein_id": "ENSP00000320919.3",
"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": "ENST00000318673.6"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NHEJ1",
"gene_hgnc_id": 25737,
"hgvs_c": "c.367T>C",
"hgvs_p": "p.Cys123Arg",
"transcript": "ENST00000881108.1",
"protein_id": "ENSP00000551167.1",
"transcript_support_level": null,
"aa_start": 123,
"aa_end": null,
"aa_length": 321,
"cds_start": 367,
"cds_end": null,
"cds_length": 966,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000881108.1"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NHEJ1",
"gene_hgnc_id": 25737,
"hgvs_c": "c.367T>C",
"hgvs_p": "p.Cys123Arg",
"transcript": "ENST00000409720.5",
"protein_id": "ENSP00000387290.1",
"transcript_support_level": 5,
"aa_start": 123,
"aa_end": null,
"aa_length": 316,
"cds_start": 367,
"cds_end": null,
"cds_length": 951,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000409720.5"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NHEJ1",
"gene_hgnc_id": 25737,
"hgvs_c": "c.367T>C",
"hgvs_p": "p.Cys123Arg",
"transcript": "NM_001377499.1",
"protein_id": "NP_001364428.1",
"transcript_support_level": null,
"aa_start": 123,
"aa_end": null,
"aa_length": 304,
"cds_start": 367,
"cds_end": null,
"cds_length": 915,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001377499.1"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NHEJ1",
"gene_hgnc_id": 25737,
"hgvs_c": "c.367T>C",
"hgvs_p": "p.Cys123Arg",
"transcript": "ENST00000426304.6",
"protein_id": "ENSP00000394896.2",
"transcript_support_level": 3,
"aa_start": 123,
"aa_end": null,
"aa_length": 304,
"cds_start": 367,
"cds_end": null,
"cds_length": 915,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000426304.6"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NHEJ1",
"gene_hgnc_id": 25737,
"hgvs_c": "c.367T>C",
"hgvs_p": "p.Cys123Arg",
"transcript": "ENST00000929435.1",
"protein_id": "ENSP00000599494.1",
"transcript_support_level": null,
"aa_start": 123,
"aa_end": null,
"aa_length": 304,
"cds_start": 367,
"cds_end": null,
"cds_length": 915,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000929435.1"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NHEJ1",
"gene_hgnc_id": 25737,
"hgvs_c": "c.367T>C",
"hgvs_p": "p.Cys123Arg",
"transcript": "ENST00000929436.1",
"protein_id": "ENSP00000599495.1",
"transcript_support_level": null,
"aa_start": 123,
"aa_end": null,
"aa_length": 304,
"cds_start": 367,
"cds_end": null,
"cds_length": 915,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000929436.1"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NHEJ1",
"gene_hgnc_id": 25737,
"hgvs_c": "c.367T>C",
"hgvs_p": "p.Cys123Arg",
"transcript": "NM_001377498.1",
"protein_id": "NP_001364427.1",
"transcript_support_level": null,
"aa_start": 123,
"aa_end": null,
"aa_length": 299,
"cds_start": 367,
"cds_end": null,
"cds_length": 900,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001377498.1"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NHEJ1",
"gene_hgnc_id": 25737,
"hgvs_c": "c.367T>C",
"hgvs_p": "p.Cys123Arg",
"transcript": "ENST00000457600.3",
"protein_id": "ENSP00000407201.2",
"transcript_support_level": 3,
"aa_start": 123,
"aa_end": null,
"aa_length": 299,
"cds_start": 367,
"cds_end": null,
"cds_length": 900,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000457600.3"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NHEJ1",
"gene_hgnc_id": 25737,
"hgvs_c": "c.367T>C",
"hgvs_p": "p.Cys123Arg",
"transcript": "ENST00000881109.1",
"protein_id": "ENSP00000551168.1",
"transcript_support_level": null,
"aa_start": 123,
"aa_end": null,
"aa_length": 299,
"cds_start": 367,
"cds_end": null,
"cds_length": 900,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000881109.1"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NHEJ1",
"gene_hgnc_id": 25737,
"hgvs_c": "c.367T>C",
"hgvs_p": "p.Cys123Arg",
"transcript": "ENST00000929432.1",
"protein_id": "ENSP00000599491.1",
"transcript_support_level": null,
"aa_start": 123,
"aa_end": null,
"aa_length": 299,
"cds_start": 367,
"cds_end": null,
"cds_length": 900,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000929432.1"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NHEJ1",
"gene_hgnc_id": 25737,
"hgvs_c": "c.367T>C",
"hgvs_p": "p.Cys123Arg",
"transcript": "ENST00000929437.1",
"protein_id": "ENSP00000599496.1",
"transcript_support_level": null,
"aa_start": 123,
"aa_end": null,
"aa_length": 299,
"cds_start": 367,
"cds_end": null,
"cds_length": 900,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000929437.1"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NHEJ1",
"gene_hgnc_id": 25737,
"hgvs_c": "c.367T>C",
"hgvs_p": "p.Cys123Arg",
"transcript": "ENST00000929438.1",
"protein_id": "ENSP00000599497.1",
"transcript_support_level": null,
"aa_start": 123,
"aa_end": null,
"aa_length": 299,
"cds_start": 367,
"cds_end": null,
"cds_length": 900,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000929438.1"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NHEJ1",
"gene_hgnc_id": 25737,
"hgvs_c": "c.364T>C",
"hgvs_p": "p.Cys122Arg",
"transcript": "ENST00000929433.1",
"protein_id": "ENSP00000599492.1",
"transcript_support_level": null,
"aa_start": 122,
"aa_end": null,
"aa_length": 298,
"cds_start": 364,
"cds_end": null,
"cds_length": 897,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000929433.1"
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NHEJ1",
"gene_hgnc_id": 25737,
"hgvs_c": "c.367T>C",
"hgvs_p": "p.Cys123Arg",
"transcript": "ENST00000929434.1",
"protein_id": "ENSP00000599493.1",
"transcript_support_level": null,
"aa_start": 123,
"aa_end": null,
"aa_length": 298,
"cds_start": 367,
"cds_end": null,
"cds_length": 897,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000929434.1"
},
{
"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": 7,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "NHEJ1",
"gene_hgnc_id": 25737,
"hgvs_c": "c.177+691T>C",
"hgvs_p": null,
"transcript": "ENST00000941811.1",
"protein_id": "ENSP00000611870.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 228,
"cds_start": null,
"cds_end": null,
"cds_length": 687,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000941811.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NHEJ1",
"gene_hgnc_id": 25737,
"hgvs_c": "n.367T>C",
"hgvs_p": null,
"transcript": "ENST00000418099.5",
"protein_id": "ENSP00000408966.1",
"transcript_support_level": 5,
"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": "ENST00000418099.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"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": "NHEJ1",
"gene_hgnc_id": 25737,
"hgvs_c": "n.*54T>C",
"hgvs_p": null,
"transcript": "ENST00000450447.1",
"protein_id": "ENSP00000408421.1",
"transcript_support_level": 4,
"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": "ENST00000450447.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000280537",
"gene_hgnc_id": null,
"hgvs_c": "n.2555T>C",
"hgvs_p": null,
"transcript": "ENST00000498327.5",
"protein_id": null,
"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": "retained_intron",
"feature": "ENST00000498327.5"
},
{
"aa_ref": null,
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"dbsnp": "rs118204452",
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"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.0000013683,
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"gnomad_exomes_ac": 2,
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"gnomad_exomes_homalt": 0,
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"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9841991066932678,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.743,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9623,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.29,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.439,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
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"dbscsnv_ada_prediction": null,
"apogee2_score": null,
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"mitotip_score": null,
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"acmg_score": 7,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_001377499.1",
"gene_symbol": "NHEJ1",
"hgnc_id": 25737,
"effects": [
"missense_variant"
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"inheritance_mode": "AR",
"hgvs_c": "c.367T>C",
"hgvs_p": "p.Cys123Arg"
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{
"score": 7,
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"criteria": [
"PM2",
"PP3_Strong",
"PP5"
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"verdict": "Likely_pathogenic",
"transcript": "ENST00000318673.6",
"gene_symbol": "ENSG00000280537",
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"effects": [
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],
"inheritance_mode": "",
"hgvs_c": "n.*1489T>C",
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}
],
"clinvar_disease": "Cernunnos-XLF deficiency",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Cernunnos-XLF deficiency",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}