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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: 3-112168889-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=112168889&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 112168889,
"ref": "T",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "NM_183061.3",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9C1",
"gene_hgnc_id": 31401,
"hgvs_c": "c.3225A>T",
"hgvs_p": "p.Ile1075Ile",
"transcript": "NM_183061.3",
"protein_id": "NP_898884.1",
"transcript_support_level": null,
"aa_start": 1075,
"aa_end": null,
"aa_length": 1177,
"cds_start": 3225,
"cds_end": null,
"cds_length": 3534,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000305815.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_183061.3"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9C1",
"gene_hgnc_id": 31401,
"hgvs_c": "c.3225A>T",
"hgvs_p": "p.Ile1075Ile",
"transcript": "ENST00000305815.10",
"protein_id": "ENSP00000306627.5",
"transcript_support_level": 2,
"aa_start": 1075,
"aa_end": null,
"aa_length": 1177,
"cds_start": 3225,
"cds_end": null,
"cds_length": 3534,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_183061.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000305815.10"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9C1",
"gene_hgnc_id": 31401,
"hgvs_c": "c.3081A>T",
"hgvs_p": "p.Ile1027Ile",
"transcript": "ENST00000487372.5",
"protein_id": "ENSP00000420688.1",
"transcript_support_level": 1,
"aa_start": 1027,
"aa_end": null,
"aa_length": 1129,
"cds_start": 3081,
"cds_end": null,
"cds_length": 3390,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000487372.5"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9C1",
"gene_hgnc_id": 31401,
"hgvs_c": "c.3081A>T",
"hgvs_p": "p.Ile1027Ile",
"transcript": "NM_001320531.2",
"protein_id": "NP_001307460.1",
"transcript_support_level": null,
"aa_start": 1027,
"aa_end": null,
"aa_length": 1129,
"cds_start": 3081,
"cds_end": null,
"cds_length": 3390,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001320531.2"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9C1",
"gene_hgnc_id": 31401,
"hgvs_c": "c.3096A>T",
"hgvs_p": "p.Ile1032Ile",
"transcript": "XM_017006246.2",
"protein_id": "XP_016861735.1",
"transcript_support_level": null,
"aa_start": 1032,
"aa_end": null,
"aa_length": 1134,
"cds_start": 3096,
"cds_end": null,
"cds_length": 3405,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017006246.2"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9C1",
"gene_hgnc_id": 31401,
"hgvs_c": "c.3063A>T",
"hgvs_p": "p.Ile1021Ile",
"transcript": "XM_011512718.2",
"protein_id": "XP_011511020.1",
"transcript_support_level": null,
"aa_start": 1021,
"aa_end": null,
"aa_length": 1123,
"cds_start": 3063,
"cds_end": null,
"cds_length": 3372,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011512718.2"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9C1",
"gene_hgnc_id": 31401,
"hgvs_c": "c.3054A>T",
"hgvs_p": "p.Ile1018Ile",
"transcript": "XM_011512719.2",
"protein_id": "XP_011511021.1",
"transcript_support_level": null,
"aa_start": 1018,
"aa_end": null,
"aa_length": 1120,
"cds_start": 3054,
"cds_end": null,
"cds_length": 3363,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011512719.2"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9C1",
"gene_hgnc_id": 31401,
"hgvs_c": "c.3039A>T",
"hgvs_p": "p.Ile1013Ile",
"transcript": "XM_017006247.2",
"protein_id": "XP_016861736.1",
"transcript_support_level": null,
"aa_start": 1013,
"aa_end": null,
"aa_length": 1115,
"cds_start": 3039,
"cds_end": null,
"cds_length": 3348,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017006247.2"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9C1",
"gene_hgnc_id": 31401,
"hgvs_c": "c.2829A>T",
"hgvs_p": "p.Ile943Ile",
"transcript": "XM_017006248.2",
"protein_id": "XP_016861737.1",
"transcript_support_level": null,
"aa_start": 943,
"aa_end": null,
"aa_length": 1045,
"cds_start": 2829,
"cds_end": null,
"cds_length": 3138,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017006248.2"
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9C1",
"gene_hgnc_id": 31401,
"hgvs_c": "c.1818A>T",
"hgvs_p": "p.Ile606Ile",
"transcript": "XM_011512725.2",
"protein_id": "XP_011511027.1",
"transcript_support_level": null,
"aa_start": 606,
"aa_end": null,
"aa_length": 708,
"cds_start": 1818,
"cds_end": null,
"cds_length": 2127,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011512725.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9C1",
"gene_hgnc_id": 31401,
"hgvs_c": "n.*1554A>T",
"hgvs_p": null,
"transcript": "ENST00000471295.1",
"protein_id": "ENSP00000418371.1",
"transcript_support_level": 5,
"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": "nonsense_mediated_decay",
"feature": "ENST00000471295.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9C1",
"gene_hgnc_id": 31401,
"hgvs_c": "n.2495A>T",
"hgvs_p": null,
"transcript": "NR_135297.2",
"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": "pseudogene",
"feature": "NR_135297.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9C1",
"gene_hgnc_id": 31401,
"hgvs_c": "n.*1554A>T",
"hgvs_p": null,
"transcript": "ENST00000471295.1",
"protein_id": "ENSP00000418371.1",
"transcript_support_level": 5,
"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": "nonsense_mediated_decay",
"feature": "ENST00000471295.1"
}
],
"gene_symbol": "SLC9C1",
"gene_hgnc_id": 31401,
"dbsnp": "rs762257130",
"frequency_reference_population": 0.0000027790902,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 0.00000277909,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.6299999952316284,
"computational_prediction_selected": "Benign",
"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": -0.63,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.885,
"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": -3,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP7",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 5,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "NM_183061.3",
"gene_symbol": "SLC9C1",
"hgnc_id": 31401,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.3225A>T",
"hgvs_p": "p.Ile1075Ile"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}