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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: 7-38728758-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=38728758&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "VPS41",
"hgnc_id": 12713,
"hgvs_c": "c.2293G>A",
"hgvs_p": "p.Val765Ile",
"inheritance_mode": "Unknown,AR",
"pathogenic_score": 2,
"score": 2,
"transcript": "NM_014396.4",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_score": 2,
"allele_count_reference_population": 71,
"alphamissense_prediction": null,
"alphamissense_score": 0.185,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.27,
"chr": "7",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Inborn genetic diseases",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.5320406556129456,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 854,
"aa_ref": "V",
"aa_start": 765,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5854,
"cdna_start": 2310,
"cds_end": null,
"cds_length": 2565,
"cds_start": 2293,
"consequences": [
"missense_variant"
],
"exon_count": 29,
"exon_rank": 26,
"exon_rank_end": null,
"feature": "NM_014396.4",
"gene_hgnc_id": 12713,
"gene_symbol": "VPS41",
"hgvs_c": "c.2293G>A",
"hgvs_p": "p.Val765Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000310301.9",
"protein_coding": true,
"protein_id": "NP_055211.2",
"strand": false,
"transcript": "NM_014396.4",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 854,
"aa_ref": "V",
"aa_start": 765,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5854,
"cdna_start": 2310,
"cds_end": null,
"cds_length": 2565,
"cds_start": 2293,
"consequences": [
"missense_variant"
],
"exon_count": 29,
"exon_rank": 26,
"exon_rank_end": null,
"feature": "ENST00000310301.9",
"gene_hgnc_id": 12713,
"gene_symbol": "VPS41",
"hgvs_c": "c.2293G>A",
"hgvs_p": "p.Val765Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_014396.4",
"protein_coding": true,
"protein_id": "ENSP00000309457.4",
"strand": false,
"transcript": "ENST00000310301.9",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 711,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000448833.5",
"gene_hgnc_id": 12713,
"gene_symbol": "VPS41",
"hgvs_c": "n.334G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000391980.1",
"strand": false,
"transcript": "ENST00000448833.5",
"transcript_support_level": 1
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 886,
"aa_ref": "V",
"aa_start": 797,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3369,
"cdna_start": 2406,
"cds_end": null,
"cds_length": 2661,
"cds_start": 2389,
"consequences": [
"missense_variant"
],
"exon_count": 30,
"exon_rank": 27,
"exon_rank_end": null,
"feature": "ENST00000951460.1",
"gene_hgnc_id": 12713,
"gene_symbol": "VPS41",
"hgvs_c": "c.2389G>A",
"hgvs_p": "p.Val797Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000621519.1",
"strand": false,
"transcript": "ENST00000951460.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 862,
"aa_ref": "V",
"aa_start": 773,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3297,
"cdna_start": 2334,
"cds_end": null,
"cds_length": 2589,
"cds_start": 2317,
"consequences": [
"missense_variant"
],
"exon_count": 30,
"exon_rank": 27,
"exon_rank_end": null,
"feature": "ENST00000862388.1",
"gene_hgnc_id": 12713,
"gene_symbol": "VPS41",
"hgvs_c": "c.2317G>A",
"hgvs_p": "p.Val773Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000532447.1",
"strand": false,
"transcript": "ENST00000862388.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 852,
"aa_ref": "V",
"aa_start": 765,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4209,
"cdna_start": 2310,
"cds_end": null,
"cds_length": 2559,
"cds_start": 2293,
"consequences": [
"missense_variant"
],
"exon_count": 29,
"exon_rank": 26,
"exon_rank_end": null,
"feature": "ENST00000951459.1",
"gene_hgnc_id": 12713,
"gene_symbol": "VPS41",
"hgvs_c": "c.2293G>A",
"hgvs_p": "p.Val765Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000621518.1",
"strand": false,
"transcript": "ENST00000951459.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 851,
"aa_ref": "V",
"aa_start": 762,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3157,
"cdna_start": 2301,
"cds_end": null,
"cds_length": 2556,
"cds_start": 2284,
"consequences": [
"missense_variant"
],
"exon_count": 29,
"exon_rank": 26,
"exon_rank_end": null,
"feature": "ENST00000951462.1",
"gene_hgnc_id": 12713,
"gene_symbol": "VPS41",
"hgvs_c": "c.2284G>A",
"hgvs_p": "p.Val762Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000621521.1",
"strand": false,
"transcript": "ENST00000951462.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 849,
"aa_ref": "V",
"aa_start": 765,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4227,
"cdna_start": 2310,
"cds_end": null,
"cds_length": 2550,
"cds_start": 2293,
"consequences": [
"missense_variant"
],
"exon_count": 29,
"exon_rank": 26,
"exon_rank_end": null,
"feature": "ENST00000862386.1",
"gene_hgnc_id": 12713,
"gene_symbol": "VPS41",
"hgvs_c": "c.2293G>A",
"hgvs_p": "p.Val765Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000532445.1",
"strand": false,
"transcript": "ENST00000862386.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 839,
"aa_ref": "V",
"aa_start": 765,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3223,
"cdna_start": 2310,
"cds_end": null,
"cds_length": 2520,
"cds_start": 2293,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 26,
"exon_rank_end": null,
"feature": "ENST00000862390.1",
"gene_hgnc_id": 12713,
"gene_symbol": "VPS41",
"hgvs_c": "c.2293G>A",
"hgvs_p": "p.Val765Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000532449.1",
"strand": false,
"transcript": "ENST00000862390.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 837,
"aa_ref": "V",
"aa_start": 748,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3212,
"cdna_start": 2250,
"cds_end": null,
"cds_length": 2514,
"cds_start": 2242,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 25,
"exon_rank_end": null,
"feature": "ENST00000951461.1",
"gene_hgnc_id": 12713,
"gene_symbol": "VPS41",
"hgvs_c": "c.2242G>A",
"hgvs_p": "p.Val748Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000621520.1",
"strand": false,
"transcript": "ENST00000951461.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 829,
"aa_ref": "V",
"aa_start": 740,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5779,
"cdna_start": 2235,
"cds_end": null,
"cds_length": 2490,
"cds_start": 2218,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 25,
"exon_rank_end": null,
"feature": "NM_080631.4",
"gene_hgnc_id": 12713,
"gene_symbol": "VPS41",
"hgvs_c": "c.2218G>A",
"hgvs_p": "p.Val740Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_542198.2",
"strand": false,
"transcript": "NM_080631.4",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 829,
"aa_ref": "V",
"aa_start": 740,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3181,
"cdna_start": 2218,
"cds_end": null,
"cds_length": 2490,
"cds_start": 2218,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 25,
"exon_rank_end": null,
"feature": "ENST00000395969.6",
"gene_hgnc_id": 12713,
"gene_symbol": "VPS41",
"hgvs_c": "c.2218G>A",
"hgvs_p": "p.Val740Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000379297.2",
"strand": false,
"transcript": "ENST00000395969.6",
"transcript_support_level": 5
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 828,
"aa_ref": "V",
"aa_start": 739,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3190,
"cdna_start": 2232,
"cds_end": null,
"cds_length": 2487,
"cds_start": 2215,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 25,
"exon_rank_end": null,
"feature": "ENST00000862391.1",
"gene_hgnc_id": 12713,
"gene_symbol": "VPS41",
"hgvs_c": "c.2215G>A",
"hgvs_p": "p.Val739Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000532450.1",
"strand": false,
"transcript": "ENST00000862391.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 816,
"aa_ref": "V",
"aa_start": 727,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3159,
"cdna_start": 2196,
"cds_end": null,
"cds_length": 2451,
"cds_start": 2179,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 24,
"exon_rank_end": null,
"feature": "ENST00000862389.1",
"gene_hgnc_id": 12713,
"gene_symbol": "VPS41",
"hgvs_c": "c.2179G>A",
"hgvs_p": "p.Val727Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000532448.1",
"strand": false,
"transcript": "ENST00000862389.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 811,
"aa_ref": "V",
"aa_start": 722,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4096,
"cdna_start": 2172,
"cds_end": null,
"cds_length": 2436,
"cds_start": 2164,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 24,
"exon_rank_end": null,
"feature": "ENST00000934107.1",
"gene_hgnc_id": 12713,
"gene_symbol": "VPS41",
"hgvs_c": "c.2164G>A",
"hgvs_p": "p.Val722Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000604166.1",
"strand": false,
"transcript": "ENST00000934107.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 765,
"aa_ref": "V",
"aa_start": 676,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4574,
"cdna_start": 2043,
"cds_end": null,
"cds_length": 2298,
"cds_start": 2026,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 24,
"exon_rank_end": null,
"feature": "ENST00000862385.1",
"gene_hgnc_id": 12713,
"gene_symbol": "VPS41",
"hgvs_c": "c.2026G>A",
"hgvs_p": "p.Val676Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000532444.1",
"strand": false,
"transcript": "ENST00000862385.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 763,
"aa_ref": "V",
"aa_start": 674,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3969,
"cdna_start": 2037,
"cds_end": null,
"cds_length": 2292,
"cds_start": 2020,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 24,
"exon_rank_end": null,
"feature": "ENST00000862387.1",
"gene_hgnc_id": 12713,
"gene_symbol": "VPS41",
"hgvs_c": "c.2020G>A",
"hgvs_p": "p.Val674Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000532446.1",
"strand": false,
"transcript": "ENST00000862387.1",
"transcript_support_level": null
},
{
"aa_alt": "I",
"aa_end": null,
"aa_length": 469,
"aa_ref": "V",
"aa_start": 380,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4802,
"cdna_start": 1258,
"cds_end": null,
"cds_length": 1410,
"cds_start": 1138,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "XM_017011988.2",
"gene_hgnc_id": 12713,
"gene_symbol": "VPS41",
"hgvs_c": "c.1138G>A",
"hgvs_p": "p.Val380Ile",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016867477.1",
"strand": false,
"transcript": "XM_017011988.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 951,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000482217.1",
"gene_hgnc_id": 12713,
"gene_symbol": "VPS41",
"hgvs_c": "n.752G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000482217.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2595,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 29,
"exon_rank": 26,
"exon_rank_end": null,
"feature": "XR_007060008.1",
"gene_hgnc_id": 12713,
"gene_symbol": "VPS41",
"hgvs_c": "n.2310G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "XR_007060008.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs199884913",
"effect": "missense_variant",
"frequency_reference_population": 0.00004399047,
"gene_hgnc_id": 12713,
"gene_symbol": "VPS41",
"gnomad_exomes_ac": 63,
"gnomad_exomes_af": 0.0000430958,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 8,
"gnomad_genomes_af": 0.000052588,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "Inborn genetic diseases",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 7.568,
"pos": 38728758,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.196,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.11999999731779099,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.12,
"transcript": "NM_014396.4"
}
]
}