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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: 2-65021067-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=65021067&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 65021067,
"ref": "C",
"alt": "A",
"effect": "stop_gained",
"transcript": "ENST00000234256.4",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC1A4",
"gene_hgnc_id": 10942,
"hgvs_c": "c.1520C>A",
"hgvs_p": "p.Ser507*",
"transcript": "NM_003038.5",
"protein_id": "NP_003029.2",
"transcript_support_level": null,
"aa_start": 507,
"aa_end": null,
"aa_length": 532,
"cds_start": 1520,
"cds_end": null,
"cds_length": 1599,
"cdna_start": 1765,
"cdna_end": null,
"cdna_length": 4563,
"mane_select": "ENST00000234256.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC1A4",
"gene_hgnc_id": 10942,
"hgvs_c": "c.1520C>A",
"hgvs_p": "p.Ser507*",
"transcript": "ENST00000234256.4",
"protein_id": "ENSP00000234256.3",
"transcript_support_level": 1,
"aa_start": 507,
"aa_end": null,
"aa_length": 532,
"cds_start": 1520,
"cds_end": null,
"cds_length": 1599,
"cdna_start": 1765,
"cdna_end": null,
"cdna_length": 4563,
"mane_select": "NM_003038.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC1A4",
"gene_hgnc_id": 10942,
"hgvs_c": "c.860C>A",
"hgvs_p": "p.Ser287*",
"transcript": "NM_001348406.2",
"protein_id": "NP_001335335.1",
"transcript_support_level": null,
"aa_start": 287,
"aa_end": null,
"aa_length": 312,
"cds_start": 860,
"cds_end": null,
"cds_length": 939,
"cdna_start": 1135,
"cdna_end": null,
"cdna_length": 3933,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC1A4",
"gene_hgnc_id": 10942,
"hgvs_c": "c.860C>A",
"hgvs_p": "p.Ser287*",
"transcript": "NM_001348407.2",
"protein_id": "NP_001335336.1",
"transcript_support_level": null,
"aa_start": 287,
"aa_end": null,
"aa_length": 312,
"cds_start": 860,
"cds_end": null,
"cds_length": 939,
"cdna_start": 1069,
"cdna_end": null,
"cdna_length": 3867,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC1A4",
"gene_hgnc_id": 10942,
"hgvs_c": "c.626C>A",
"hgvs_p": "p.Ser209*",
"transcript": "NM_001193493.2",
"protein_id": "NP_001180422.1",
"transcript_support_level": null,
"aa_start": 209,
"aa_end": null,
"aa_length": 234,
"cds_start": 626,
"cds_end": null,
"cds_length": 705,
"cdna_start": 901,
"cdna_end": null,
"cdna_length": 3699,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC1A4",
"gene_hgnc_id": 10942,
"hgvs_c": "c.626C>A",
"hgvs_p": "p.Ser209*",
"transcript": "ENST00000531327.5",
"protein_id": "ENSP00000431942.1",
"transcript_support_level": 2,
"aa_start": 209,
"aa_end": null,
"aa_length": 234,
"cds_start": 626,
"cds_end": null,
"cds_length": 705,
"cdna_start": 890,
"cdna_end": null,
"cdna_length": 1217,
"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": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC1A4",
"gene_hgnc_id": 10942,
"hgvs_c": "n.2993C>A",
"hgvs_p": null,
"transcript": "ENST00000480594.1",
"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": 5789,
"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": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LINC02245",
"gene_hgnc_id": 53134,
"hgvs_c": "n.513+26887G>T",
"hgvs_p": null,
"transcript": "ENST00000653778.1",
"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": 2026,
"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": 1,
"intron_rank_end": null,
"gene_symbol": "LINC02245",
"gene_hgnc_id": 53134,
"hgvs_c": "n.226+26887G>T",
"hgvs_p": null,
"transcript": "ENST00000669631.1",
"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": 1409,
"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": 2,
"intron_rank_end": null,
"gene_symbol": "LINC02245",
"gene_hgnc_id": 53134,
"hgvs_c": "n.573+26887G>T",
"hgvs_p": null,
"transcript": "ENST00000771808.1",
"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": 1506,
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LINC02245",
"gene_hgnc_id": 53134,
"hgvs_c": "n.259+26887G>T",
"hgvs_p": null,
"transcript": "ENST00000771809.1",
"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": 1333,
"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": "LINC02245",
"gene_hgnc_id": 53134,
"hgvs_c": "n.683-92G>T",
"hgvs_p": null,
"transcript": "ENST00000771811.1",
"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": 1416,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SLC1A4",
"gene_hgnc_id": 10942,
"dbsnp": "rs200617042",
"frequency_reference_population": 0.00011027872,
"hom_count_reference_population": 1,
"allele_count_reference_population": 178,
"gnomad_exomes_af": 0.000109448,
"gnomad_genomes_af": 0.000118256,
"gnomad_exomes_ac": 160,
"gnomad_genomes_ac": 18,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5699999928474426,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.57,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.035,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PVS1_Moderate",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PVS1_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000234256.4",
"gene_symbol": "SLC1A4",
"hgnc_id": 10942,
"effects": [
"stop_gained"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.1520C>A",
"hgvs_p": "p.Ser507*"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000653778.1",
"gene_symbol": "LINC02245",
"hgnc_id": 53134,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.513+26887G>T",
"hgvs_p": null
}
],
"clinvar_disease": "Spastic tetraplegia-thin corpus callosum-progressive postnatal microcephaly syndrome,not provided,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"phenotype_combined": "not specified|Spastic tetraplegia-thin corpus callosum-progressive postnatal microcephaly syndrome|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}