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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: 18-6980524-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=18&pos=6980524&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "18",
"pos": 6980524,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_005559.4",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 42,
"exon_rank_end": null,
"exon_count": 63,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMA1",
"gene_hgnc_id": 6481,
"hgvs_c": "c.6004A>G",
"hgvs_p": "p.Lys2002Glu",
"transcript": "NM_005559.4",
"protein_id": "NP_005550.2",
"transcript_support_level": null,
"aa_start": 2002,
"aa_end": null,
"aa_length": 3075,
"cds_start": 6004,
"cds_end": null,
"cds_length": 9228,
"cdna_start": 6081,
"cdna_end": null,
"cdna_length": 9642,
"mane_select": "ENST00000389658.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005559.4"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 42,
"exon_rank_end": null,
"exon_count": 63,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMA1",
"gene_hgnc_id": 6481,
"hgvs_c": "c.6004A>G",
"hgvs_p": "p.Lys2002Glu",
"transcript": "ENST00000389658.4",
"protein_id": "ENSP00000374309.3",
"transcript_support_level": 1,
"aa_start": 2002,
"aa_end": null,
"aa_length": 3075,
"cds_start": 6004,
"cds_end": null,
"cds_length": 9228,
"cdna_start": 6081,
"cdna_end": null,
"cdna_length": 9642,
"mane_select": "NM_005559.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000389658.4"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 43,
"exon_rank_end": null,
"exon_count": 64,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMA1",
"gene_hgnc_id": 6481,
"hgvs_c": "c.6097A>G",
"hgvs_p": "p.Lys2033Glu",
"transcript": "ENST00000940203.1",
"protein_id": "ENSP00000610262.1",
"transcript_support_level": null,
"aa_start": 2033,
"aa_end": null,
"aa_length": 3106,
"cds_start": 6097,
"cds_end": null,
"cds_length": 9321,
"cdna_start": 6182,
"cdna_end": null,
"cdna_length": 9597,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940203.1"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 42,
"exon_rank_end": null,
"exon_count": 63,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMA1",
"gene_hgnc_id": 6481,
"hgvs_c": "c.6004A>G",
"hgvs_p": "p.Lys2002Glu",
"transcript": "ENST00000940200.1",
"protein_id": "ENSP00000610259.1",
"transcript_support_level": null,
"aa_start": 2002,
"aa_end": null,
"aa_length": 3085,
"cds_start": 6004,
"cds_end": null,
"cds_length": 9258,
"cdna_start": 6143,
"cdna_end": null,
"cdna_length": 9732,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940200.1"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 41,
"exon_rank_end": null,
"exon_count": 62,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMA1",
"gene_hgnc_id": 6481,
"hgvs_c": "c.5866A>G",
"hgvs_p": "p.Lys1956Glu",
"transcript": "ENST00000940202.1",
"protein_id": "ENSP00000610261.1",
"transcript_support_level": null,
"aa_start": 1956,
"aa_end": null,
"aa_length": 3029,
"cds_start": 5866,
"cds_end": null,
"cds_length": 9090,
"cdna_start": 5985,
"cdna_end": null,
"cdna_length": 9402,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940202.1"
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 36,
"exon_rank_end": null,
"exon_count": 57,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMA1",
"gene_hgnc_id": 6481,
"hgvs_c": "c.5152A>G",
"hgvs_p": "p.Lys1718Glu",
"transcript": "ENST00000940201.1",
"protein_id": "ENSP00000610260.1",
"transcript_support_level": null,
"aa_start": 1718,
"aa_end": null,
"aa_length": 2791,
"cds_start": 5152,
"cds_end": null,
"cds_length": 8376,
"cdna_start": 5269,
"cdna_end": null,
"cdna_length": 8691,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940201.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 41,
"exon_rank_end": null,
"exon_count": 62,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAMA1",
"gene_hgnc_id": 6481,
"hgvs_c": "n.7019A>G",
"hgvs_p": null,
"transcript": "ENST00000579014.5",
"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": 10374,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000579014.5"
}
],
"gene_symbol": "LAMA1",
"gene_hgnc_id": 6481,
"dbsnp": "rs607230",
"frequency_reference_population": 0.71447927,
"hom_count_reference_population": 401658,
"allele_count_reference_population": 1118120,
"gnomad_exomes_af": 0.717653,
"gnomad_genomes_af": 0.684999,
"gnomad_exomes_ac": 1013922,
"gnomad_genomes_ac": 104198,
"gnomad_exomes_homalt": 365437,
"gnomad_genomes_homalt": 36221,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 6.886197070343769e-7,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.034,
"revel_prediction": "Benign",
"alphamissense_score": 0.0583,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.77,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.499,
"phylop100way_prediction": "Benign",
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_005559.4",
"gene_symbol": "LAMA1",
"hgnc_id": 6481,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.6004A>G",
"hgvs_p": "p.Lys2002Glu"
}
],
"clinvar_disease": "Ataxia - intellectual disability - oculomotor apraxia - cerebellar cysts syndrome,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:4",
"phenotype_combined": "not provided|Ataxia - intellectual disability - oculomotor apraxia - cerebellar cysts syndrome",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}