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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: 3-128056742-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=128056742&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 128056742,
"ref": "T",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000243253.8",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC61A1",
"gene_hgnc_id": 18276,
"hgvs_c": "c.254T>A",
"hgvs_p": "p.Val85Asp",
"transcript": "NM_013336.4",
"protein_id": "NP_037468.1",
"transcript_support_level": null,
"aa_start": 85,
"aa_end": null,
"aa_length": 476,
"cds_start": 254,
"cds_end": null,
"cds_length": 1431,
"cdna_start": 370,
"cdna_end": null,
"cdna_length": 3568,
"mane_select": "ENST00000243253.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC61A1",
"gene_hgnc_id": 18276,
"hgvs_c": "c.254T>A",
"hgvs_p": "p.Val85Asp",
"transcript": "ENST00000243253.8",
"protein_id": "ENSP00000243253.3",
"transcript_support_level": 1,
"aa_start": 85,
"aa_end": null,
"aa_length": 476,
"cds_start": 254,
"cds_end": null,
"cds_length": 1431,
"cdna_start": 370,
"cdna_end": null,
"cdna_length": 3568,
"mane_select": "NM_013336.4",
"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": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC61A1",
"gene_hgnc_id": 18276,
"hgvs_c": "n.254T>A",
"hgvs_p": null,
"transcript": "ENST00000483956.2",
"protein_id": "ENSP00000514247.1",
"transcript_support_level": 1,
"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": 3890,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC61A1",
"gene_hgnc_id": 18276,
"hgvs_c": "c.254T>A",
"hgvs_p": "p.Val85Asp",
"transcript": "ENST00000699273.1",
"protein_id": "ENSP00000514253.1",
"transcript_support_level": null,
"aa_start": 85,
"aa_end": null,
"aa_length": 485,
"cds_start": 254,
"cds_end": null,
"cds_length": 1458,
"cdna_start": 423,
"cdna_end": null,
"cdna_length": 3632,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC61A1",
"gene_hgnc_id": 18276,
"hgvs_c": "c.272T>A",
"hgvs_p": "p.Val91Asp",
"transcript": "NM_001400328.1",
"protein_id": "NP_001387257.1",
"transcript_support_level": null,
"aa_start": 91,
"aa_end": null,
"aa_length": 482,
"cds_start": 272,
"cds_end": null,
"cds_length": 1449,
"cdna_start": 517,
"cdna_end": null,
"cdna_length": 3715,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC61A1",
"gene_hgnc_id": 18276,
"hgvs_c": "c.272T>A",
"hgvs_p": "p.Val91Asp",
"transcript": "ENST00000464451.5",
"protein_id": "ENSP00000418493.1",
"transcript_support_level": 2,
"aa_start": 91,
"aa_end": null,
"aa_length": 482,
"cds_start": 272,
"cds_end": null,
"cds_length": 1449,
"cdna_start": 517,
"cdna_end": null,
"cdna_length": 1871,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC61A1",
"gene_hgnc_id": 18276,
"hgvs_c": "c.95T>A",
"hgvs_p": "p.Val32Asp",
"transcript": "NM_001400329.1",
"protein_id": "NP_001387258.1",
"transcript_support_level": null,
"aa_start": 32,
"aa_end": null,
"aa_length": 423,
"cds_start": 95,
"cds_end": null,
"cds_length": 1272,
"cdna_start": 302,
"cdna_end": null,
"cdna_length": 3500,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC61A1",
"gene_hgnc_id": 18276,
"hgvs_c": "c.95T>A",
"hgvs_p": "p.Val32Asp",
"transcript": "ENST00000481210.6",
"protein_id": "ENSP00000419172.2",
"transcript_support_level": 5,
"aa_start": 32,
"aa_end": null,
"aa_length": 423,
"cds_start": 95,
"cds_end": null,
"cds_length": 1272,
"cdna_start": 338,
"cdna_end": null,
"cdna_length": 3521,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC61A1",
"gene_hgnc_id": 18276,
"hgvs_c": "c.254T>A",
"hgvs_p": "p.Val85Asp",
"transcript": "ENST00000699267.1",
"protein_id": "ENSP00000514248.1",
"transcript_support_level": null,
"aa_start": 85,
"aa_end": null,
"aa_length": 415,
"cds_start": 254,
"cds_end": null,
"cds_length": 1248,
"cdna_start": 423,
"cdna_end": null,
"cdna_length": 2938,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC61A1",
"gene_hgnc_id": 18276,
"hgvs_c": "c.254T>A",
"hgvs_p": "p.Val85Asp",
"transcript": "ENST00000699269.1",
"protein_id": "ENSP00000514249.1",
"transcript_support_level": null,
"aa_start": 85,
"aa_end": null,
"aa_length": 346,
"cds_start": 254,
"cds_end": null,
"cds_length": 1041,
"cdna_start": 423,
"cdna_end": null,
"cdna_length": 3199,
"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": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC61A1",
"gene_hgnc_id": 18276,
"hgvs_c": "n.593T>A",
"hgvs_p": null,
"transcript": "ENST00000491668.2",
"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": 3776,
"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": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC61A1",
"gene_hgnc_id": 18276,
"hgvs_c": "n.423T>A",
"hgvs_p": null,
"transcript": "ENST00000699266.1",
"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": 4587,
"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": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC61A1",
"gene_hgnc_id": 18276,
"hgvs_c": "n.423T>A",
"hgvs_p": null,
"transcript": "ENST00000699268.1",
"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": 5354,
"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": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC61A1",
"gene_hgnc_id": 18276,
"hgvs_c": "n.254T>A",
"hgvs_p": null,
"transcript": "ENST00000699270.1",
"protein_id": "ENSP00000514250.1",
"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,
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"cdna_length": 3742,
"mane_select": null,
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"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": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC61A1",
"gene_hgnc_id": 18276,
"hgvs_c": "n.254T>A",
"hgvs_p": null,
"transcript": "ENST00000699271.1",
"protein_id": "ENSP00000514251.1",
"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,
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"cdna_length": 4442,
"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": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC61A1",
"gene_hgnc_id": 18276,
"hgvs_c": "n.254T>A",
"hgvs_p": null,
"transcript": "ENST00000699272.1",
"protein_id": "ENSP00000514252.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
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"cdna_length": 4452,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC61A1",
"gene_hgnc_id": 18276,
"hgvs_c": "n.254T>A",
"hgvs_p": null,
"transcript": "ENST00000699274.1",
"protein_id": "ENSP00000514254.1",
"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": 4519,
"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": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC61A1",
"gene_hgnc_id": 18276,
"hgvs_c": "n.*124T>A",
"hgvs_p": null,
"transcript": "ENST00000699275.1",
"protein_id": "ENSP00000514255.1",
"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": 3575,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC61A1",
"gene_hgnc_id": 18276,
"hgvs_c": "n.373T>A",
"hgvs_p": null,
"transcript": "ENST00000699280.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 1067,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC61A1",
"gene_hgnc_id": 18276,
"hgvs_c": "n.*124T>A",
"hgvs_p": null,
"transcript": "ENST00000699275.1",
"protein_id": "ENSP00000514255.1",
"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": 3575,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SEC61A1",
"gene_hgnc_id": 18276,
"hgvs_c": "c.-8-3360T>A",
"hgvs_p": null,
"transcript": "ENST00000424880.2",
"protein_id": "ENSP00000411445.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 356,
"cds_start": -4,
"cds_end": null,
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"cdna_start": null,
"cdna_end": null,
"cdna_length": 3238,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "SEC61A1",
"gene_hgnc_id": 18276,
"hgvs_c": "n.333+991T>A",
"hgvs_p": null,
"transcript": "ENST00000699281.1",
"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": 569,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SEC61A1",
"gene_hgnc_id": 18276,
"dbsnp": "rs1553721236",
"frequency_reference_population": null,
"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": 0.937674880027771,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.852,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9996,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.49,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 8.017,
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Moderate,PP5_Moderate",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000243253.8",
"gene_symbol": "SEC61A1",
"hgnc_id": 18276,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.254T>A",
"hgvs_p": "p.Val85Asp"
}
],
"clinvar_disease": " 15, common variable,Decreased circulating immunoglobulin concentration,Immunodeficiency",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "Decreased circulating immunoglobulin concentration|Immunodeficiency, common variable, 15",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}