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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: 9-131085653-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=131085653&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 131085653,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_006059.4",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMC3",
"gene_hgnc_id": 6494,
"hgvs_c": "c.4160C>T",
"hgvs_p": "p.Ala1387Val",
"transcript": "NM_006059.4",
"protein_id": "NP_006050.3",
"transcript_support_level": null,
"aa_start": 1387,
"aa_end": null,
"aa_length": 1575,
"cds_start": 4160,
"cds_end": null,
"cds_length": 4728,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000361069.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006059.4"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMC3",
"gene_hgnc_id": 6494,
"hgvs_c": "c.4160C>T",
"hgvs_p": "p.Ala1387Val",
"transcript": "ENST00000361069.9",
"protein_id": "ENSP00000354360.4",
"transcript_support_level": 2,
"aa_start": 1387,
"aa_end": null,
"aa_length": 1575,
"cds_start": 4160,
"cds_end": null,
"cds_length": 4728,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_006059.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000361069.9"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMC3",
"gene_hgnc_id": 6494,
"hgvs_c": "c.203C>T",
"hgvs_p": "p.Ala68Val",
"transcript": "ENST00000355452.5",
"protein_id": "ENSP00000347627.5",
"transcript_support_level": 1,
"aa_start": 68,
"aa_end": null,
"aa_length": 256,
"cds_start": 203,
"cds_end": null,
"cds_length": 771,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000355452.5"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMC3",
"gene_hgnc_id": 6494,
"hgvs_c": "c.4178C>T",
"hgvs_p": "p.Ala1393Val",
"transcript": "ENST00000868026.1",
"protein_id": "ENSP00000538085.1",
"transcript_support_level": null,
"aa_start": 1393,
"aa_end": null,
"aa_length": 1581,
"cds_start": 4178,
"cds_end": null,
"cds_length": 4746,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000868026.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMC3",
"gene_hgnc_id": 6494,
"hgvs_c": "c.4154C>T",
"hgvs_p": "p.Ala1385Val",
"transcript": "ENST00000955224.1",
"protein_id": "ENSP00000625283.1",
"transcript_support_level": null,
"aa_start": 1385,
"aa_end": null,
"aa_length": 1573,
"cds_start": 4154,
"cds_end": null,
"cds_length": 4722,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000955224.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMC3",
"gene_hgnc_id": 6494,
"hgvs_c": "c.4160C>T",
"hgvs_p": "p.Ala1387Val",
"transcript": "ENST00000955225.1",
"protein_id": "ENSP00000625284.1",
"transcript_support_level": null,
"aa_start": 1387,
"aa_end": null,
"aa_length": 1567,
"cds_start": 4160,
"cds_end": null,
"cds_length": 4704,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000955225.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMC3",
"gene_hgnc_id": 6494,
"hgvs_c": "c.4061C>T",
"hgvs_p": "p.Ala1354Val",
"transcript": "ENST00000955223.1",
"protein_id": "ENSP00000625282.1",
"transcript_support_level": null,
"aa_start": 1354,
"aa_end": null,
"aa_length": 1542,
"cds_start": 4061,
"cds_end": null,
"cds_length": 4629,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000955223.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMC3",
"gene_hgnc_id": 6494,
"hgvs_c": "c.3851C>T",
"hgvs_p": "p.Ala1284Val",
"transcript": "ENST00000940484.1",
"protein_id": "ENSP00000610543.1",
"transcript_support_level": null,
"aa_start": 1284,
"aa_end": null,
"aa_length": 1472,
"cds_start": 3851,
"cds_end": null,
"cds_length": 4419,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940484.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMC3",
"gene_hgnc_id": 6494,
"hgvs_c": "c.320C>T",
"hgvs_p": "p.Ala107Val",
"transcript": "ENST00000678758.1",
"protein_id": "ENSP00000503612.1",
"transcript_support_level": null,
"aa_start": 107,
"aa_end": null,
"aa_length": 287,
"cds_start": 320,
"cds_end": null,
"cds_length": 864,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000678758.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMC3",
"gene_hgnc_id": 6494,
"hgvs_c": "c.4178C>T",
"hgvs_p": "p.Ala1393Val",
"transcript": "XM_011518121.2",
"protein_id": "XP_011516423.1",
"transcript_support_level": null,
"aa_start": 1393,
"aa_end": null,
"aa_length": 1581,
"cds_start": 4178,
"cds_end": null,
"cds_length": 4746,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011518121.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMC3",
"gene_hgnc_id": 6494,
"hgvs_c": "n.1733C>T",
"hgvs_p": null,
"transcript": "ENST00000678544.1",
"protein_id": null,
"transcript_support_level": null,
"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": "ENST00000678544.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMC3",
"gene_hgnc_id": 6494,
"hgvs_c": "n.-172C>T",
"hgvs_p": null,
"transcript": "ENST00000462567.1",
"protein_id": null,
"transcript_support_level": 3,
"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": "pseudogene",
"feature": "ENST00000462567.1"
}
],
"gene_symbol": "LAMC3",
"gene_hgnc_id": 6494,
"dbsnp": "rs141497885",
"frequency_reference_population": 0.00071863114,
"hom_count_reference_population": 1,
"allele_count_reference_population": 1160,
"gnomad_exomes_af": 0.000585563,
"gnomad_genomes_af": 0.00199556,
"gnomad_exomes_ac": 856,
"gnomad_genomes_ac": 304,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.007573336362838745,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.229,
"revel_prediction": "Benign",
"alphamissense_score": 0.1074,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.3,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.973,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong,BP6",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "NM_006059.4",
"gene_symbol": "LAMC3",
"hgnc_id": 6494,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.4160C>T",
"hgvs_p": "p.Ala1387Val"
}
],
"clinvar_disease": "LAMC3-related disorder,Occipital pachygyria and polymicrogyria,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:3 LB:2",
"phenotype_combined": "not specified|not provided|Occipital pachygyria and polymicrogyria|LAMC3-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}