← Back to variant description
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: 19-41987936-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=41987936&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 41987936,
"ref": "G",
"alt": "A",
"effect": "splice_region_variant,synonymous_variant",
"transcript": "ENST00000648268.1",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "c.357C>T",
"hgvs_p": "p.Asn119Asn",
"transcript": "NM_152296.5",
"protein_id": "NP_689509.1",
"transcript_support_level": null,
"aa_start": 119,
"aa_end": null,
"aa_length": 1013,
"cds_start": 357,
"cds_end": null,
"cds_length": 3042,
"cdna_start": 511,
"cdna_end": null,
"cdna_length": 3551,
"mane_select": "ENST00000648268.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "c.357C>T",
"hgvs_p": "p.Asn119Asn",
"transcript": "ENST00000648268.1",
"protein_id": "ENSP00000498113.1",
"transcript_support_level": null,
"aa_start": 119,
"aa_end": null,
"aa_length": 1013,
"cds_start": 357,
"cds_end": null,
"cds_length": 3042,
"cdna_start": 511,
"cdna_end": null,
"cdna_length": 3551,
"mane_select": "NM_152296.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285505",
"gene_hgnc_id": null,
"hgvs_c": "n.357C>T",
"hgvs_p": null,
"transcript": "ENST00000644613.1",
"protein_id": "ENSP00000494711.1",
"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": 3536,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "c.396C>T",
"hgvs_p": "p.Asn132Asn",
"transcript": "NM_001256214.2",
"protein_id": "NP_001243143.1",
"transcript_support_level": null,
"aa_start": 132,
"aa_end": null,
"aa_length": 1026,
"cds_start": 396,
"cds_end": null,
"cds_length": 3081,
"cdna_start": 550,
"cdna_end": null,
"cdna_length": 3590,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "c.396C>T",
"hgvs_p": "p.Asn132Asn",
"transcript": "ENST00000545399.6",
"protein_id": "ENSP00000444688.1",
"transcript_support_level": 2,
"aa_start": 132,
"aa_end": null,
"aa_length": 1026,
"cds_start": 396,
"cds_end": null,
"cds_length": 3081,
"cdna_start": 590,
"cdna_end": null,
"cdna_length": 3628,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "c.390C>T",
"hgvs_p": "p.Asn130Asn",
"transcript": "NM_001256213.2",
"protein_id": "NP_001243142.1",
"transcript_support_level": null,
"aa_start": 130,
"aa_end": null,
"aa_length": 1024,
"cds_start": 390,
"cds_end": null,
"cds_length": 3075,
"cdna_start": 426,
"cdna_end": null,
"cdna_length": 3466,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "c.390C>T",
"hgvs_p": "p.Asn130Asn",
"transcript": "ENST00000543770.5",
"protein_id": "ENSP00000437577.1",
"transcript_support_level": 2,
"aa_start": 130,
"aa_end": null,
"aa_length": 1024,
"cds_start": 390,
"cds_end": null,
"cds_length": 3075,
"cdna_start": 426,
"cdna_end": null,
"cdna_length": 3427,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "c.267C>T",
"hgvs_p": "p.Asn89Asn",
"transcript": "ENST00000602133.5",
"protein_id": "ENSP00000471581.1",
"transcript_support_level": 2,
"aa_start": 89,
"aa_end": null,
"aa_length": 983,
"cds_start": 267,
"cds_end": null,
"cds_length": 2952,
"cdna_start": 420,
"cdna_end": null,
"cdna_length": 3458,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "c.267C>T",
"hgvs_p": "p.Asn89Asn",
"transcript": "ENST00000473086.3",
"protein_id": "ENSP00000469129.2",
"transcript_support_level": 5,
"aa_start": 89,
"aa_end": null,
"aa_length": 250,
"cds_start": 267,
"cds_end": null,
"cds_length": 754,
"cdna_start": 402,
"cdna_end": null,
"cdna_length": 889,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "c.267C>T",
"hgvs_p": "p.Asn89Asn",
"transcript": "XM_047438862.1",
"protein_id": "XP_047294818.1",
"transcript_support_level": null,
"aa_start": 89,
"aa_end": null,
"aa_length": 983,
"cds_start": 267,
"cds_end": null,
"cds_length": 2952,
"cdna_start": 370,
"cdna_end": null,
"cdna_length": 3410,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "n.357C>T",
"hgvs_p": null,
"transcript": "ENST00000441343.5",
"protein_id": "ENSP00000411503.1",
"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": 3818,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"hgvs_c": "n.*63C>T",
"hgvs_p": null,
"transcript": "ENST00000468774.3",
"protein_id": null,
"transcript_support_level": 3,
"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": 603,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ATP1A3",
"gene_hgnc_id": 801,
"dbsnp": "rs143547136",
"frequency_reference_population": 0.002231703,
"hom_count_reference_population": 16,
"allele_count_reference_population": 3601,
"gnomad_exomes_af": 0.00232875,
"gnomad_genomes_af": 0.00130036,
"gnomad_exomes_ac": 3403,
"gnomad_genomes_ac": 198,
"gnomad_exomes_homalt": 14,
"gnomad_genomes_homalt": 2,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7200000286102295,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.10400000214576721,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.72,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.525,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.000878223706301888,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000648268.1",
"gene_symbol": "ATP1A3",
"hgnc_id": 801,
"effects": [
"splice_region_variant",
"synonymous_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.357C>T",
"hgvs_p": "p.Asn119Asn"
},
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000644613.1",
"gene_symbol": "ENSG00000285505",
"hgnc_id": null,
"effects": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.357C>T",
"hgvs_p": null
}
],
"clinvar_disease": "ATP1A3-related disorder,Alternating hemiplegia of childhood 2,Cerebellar ataxia-areflexia-pes cavus-optic atrophy-sensorineural hearing loss syndrome,Developmental and epileptic encephalopathy 99,Dystonia 12,Inborn genetic diseases,not provided",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:4 B:9",
"phenotype_combined": "Dystonia 12|Alternating hemiplegia of childhood 2|not provided|Cerebellar ataxia-areflexia-pes cavus-optic atrophy-sensorineural hearing loss syndrome|Developmental and epileptic encephalopathy 99|Dystonia 12;Developmental and epileptic encephalopathy 99;Cerebellar ataxia-areflexia-pes cavus-optic atrophy-sensorineural hearing loss syndrome;Alternating hemiplegia of childhood 2|ATP1A3-related disorder|Inborn genetic diseases",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}