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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: 4-1983411-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=1983411&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 1983411,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_005663.5",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELFA",
"gene_hgnc_id": 12768,
"hgvs_c": "c.1495A>G",
"hgvs_p": "p.Thr499Ala",
"transcript": "NM_005663.5",
"protein_id": "NP_005654.4",
"transcript_support_level": null,
"aa_start": 499,
"aa_end": null,
"aa_length": 528,
"cds_start": 1495,
"cds_end": null,
"cds_length": 1587,
"cdna_start": 1510,
"cdna_end": null,
"cdna_length": 2198,
"mane_select": "ENST00000382882.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005663.5"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELFA",
"gene_hgnc_id": 12768,
"hgvs_c": "c.1495A>G",
"hgvs_p": "p.Thr499Ala",
"transcript": "ENST00000382882.9",
"protein_id": "ENSP00000372335.4",
"transcript_support_level": 1,
"aa_start": 499,
"aa_end": null,
"aa_length": 528,
"cds_start": 1495,
"cds_end": null,
"cds_length": 1587,
"cdna_start": 1510,
"cdna_end": null,
"cdna_length": 2198,
"mane_select": "NM_005663.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000382882.9"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELFA",
"gene_hgnc_id": 12768,
"hgvs_c": "c.1528A>G",
"hgvs_p": "p.Thr510Ala",
"transcript": "ENST00000542778.5",
"protein_id": "ENSP00000445757.2",
"transcript_support_level": 1,
"aa_start": 510,
"aa_end": null,
"aa_length": 539,
"cds_start": 1528,
"cds_end": null,
"cds_length": 1620,
"cdna_start": 1771,
"cdna_end": null,
"cdna_length": 2465,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000542778.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELFA",
"gene_hgnc_id": 12768,
"hgvs_c": "n.1019A>G",
"hgvs_p": null,
"transcript": "ENST00000467661.5",
"protein_id": null,
"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": 1707,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000467661.5"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELFA",
"gene_hgnc_id": 12768,
"hgvs_c": "c.1615A>G",
"hgvs_p": "p.Thr539Ala",
"transcript": "ENST00000898322.1",
"protein_id": "ENSP00000568381.1",
"transcript_support_level": null,
"aa_start": 539,
"aa_end": null,
"aa_length": 568,
"cds_start": 1615,
"cds_end": null,
"cds_length": 1707,
"cdna_start": 1630,
"cdna_end": null,
"cdna_length": 2318,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898322.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELFA",
"gene_hgnc_id": 12768,
"hgvs_c": "c.1579A>G",
"hgvs_p": "p.Thr527Ala",
"transcript": "ENST00000898321.1",
"protein_id": "ENSP00000568380.1",
"transcript_support_level": null,
"aa_start": 527,
"aa_end": null,
"aa_length": 556,
"cds_start": 1579,
"cds_end": null,
"cds_length": 1671,
"cdna_start": 1594,
"cdna_end": null,
"cdna_length": 2282,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898321.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELFA",
"gene_hgnc_id": 12768,
"hgvs_c": "c.1507A>G",
"hgvs_p": "p.Thr503Ala",
"transcript": "ENST00000416258.5",
"protein_id": "ENSP00000387647.1",
"transcript_support_level": 5,
"aa_start": 503,
"aa_end": null,
"aa_length": 532,
"cds_start": 1507,
"cds_end": null,
"cds_length": 1599,
"cdna_start": 1507,
"cdna_end": null,
"cdna_length": 2188,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000416258.5"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELFA",
"gene_hgnc_id": 12768,
"hgvs_c": "c.1501A>G",
"hgvs_p": "p.Thr501Ala",
"transcript": "ENST00000911416.1",
"protein_id": "ENSP00000581475.1",
"transcript_support_level": null,
"aa_start": 501,
"aa_end": null,
"aa_length": 530,
"cds_start": 1501,
"cds_end": null,
"cds_length": 1593,
"cdna_start": 1516,
"cdna_end": null,
"cdna_length": 2204,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911416.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELFA",
"gene_hgnc_id": 12768,
"hgvs_c": "c.1489A>G",
"hgvs_p": "p.Thr497Ala",
"transcript": "ENST00000898320.1",
"protein_id": "ENSP00000568379.1",
"transcript_support_level": null,
"aa_start": 497,
"aa_end": null,
"aa_length": 526,
"cds_start": 1489,
"cds_end": null,
"cds_length": 1581,
"cdna_start": 1517,
"cdna_end": null,
"cdna_length": 2209,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898320.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELFA",
"gene_hgnc_id": 12768,
"hgvs_c": "c.1465A>G",
"hgvs_p": "p.Thr489Ala",
"transcript": "ENST00000967102.1",
"protein_id": "ENSP00000637161.1",
"transcript_support_level": null,
"aa_start": 489,
"aa_end": null,
"aa_length": 518,
"cds_start": 1465,
"cds_end": null,
"cds_length": 1557,
"cdna_start": 1480,
"cdna_end": null,
"cdna_length": 2165,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000967102.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELFA",
"gene_hgnc_id": 12768,
"hgvs_c": "c.1417A>G",
"hgvs_p": "p.Thr473Ala",
"transcript": "ENST00000967101.1",
"protein_id": "ENSP00000637160.1",
"transcript_support_level": null,
"aa_start": 473,
"aa_end": null,
"aa_length": 502,
"cds_start": 1417,
"cds_end": null,
"cds_length": 1509,
"cdna_start": 1430,
"cdna_end": null,
"cdna_length": 2118,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000967101.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELFA",
"gene_hgnc_id": 12768,
"hgvs_c": "c.1333A>G",
"hgvs_p": "p.Thr445Ala",
"transcript": "ENST00000967103.1",
"protein_id": "ENSP00000637162.1",
"transcript_support_level": null,
"aa_start": 445,
"aa_end": null,
"aa_length": 474,
"cds_start": 1333,
"cds_end": null,
"cds_length": 1425,
"cdna_start": 1346,
"cdna_end": null,
"cdna_length": 2026,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000967103.1"
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELFA",
"gene_hgnc_id": 12768,
"hgvs_c": "c.1579A>G",
"hgvs_p": "p.Thr527Ala",
"transcript": "XM_017008589.3",
"protein_id": "XP_016864078.2",
"transcript_support_level": null,
"aa_start": 527,
"aa_end": null,
"aa_length": 556,
"cds_start": 1579,
"cds_end": null,
"cds_length": 1671,
"cdna_start": 1594,
"cdna_end": null,
"cdna_length": 2282,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017008589.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELFA",
"gene_hgnc_id": 12768,
"hgvs_c": "n.*1062A>G",
"hgvs_p": null,
"transcript": "ENST00000333877.8",
"protein_id": "ENSP00000330311.4",
"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": 2228,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000333877.8"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELFA",
"gene_hgnc_id": 12768,
"hgvs_c": "n.1814A>G",
"hgvs_p": null,
"transcript": "ENST00000463820.5",
"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": 2495,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000463820.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NELFA",
"gene_hgnc_id": 12768,
"hgvs_c": "n.*1062A>G",
"hgvs_p": null,
"transcript": "ENST00000333877.8",
"protein_id": "ENSP00000330311.4",
"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": 2228,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000333877.8"
}
],
"gene_symbol": "NELFA",
"gene_hgnc_id": 12768,
"dbsnp": "rs1334280961",
"frequency_reference_population": 0.0000027362103,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 0.00000273621,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.4515259265899658,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.344,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.0762,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.12,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.938,
"phylop100way_prediction": "Pathogenic",
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_005663.5",
"gene_symbol": "NELFA",
"hgnc_id": 12768,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1495A>G",
"hgvs_p": "p.Thr499Ala"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}