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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: 11-6392136-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=6392136&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 6392136,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001318088.2",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPD1",
"gene_hgnc_id": 11120,
"hgvs_c": "c.1071C>T",
"hgvs_p": "p.Ala357Ala",
"transcript": "NM_000543.5",
"protein_id": "NP_000534.3",
"transcript_support_level": null,
"aa_start": 357,
"aa_end": null,
"aa_length": 631,
"cds_start": 1071,
"cds_end": null,
"cds_length": 1896,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000342245.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000543.5"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPD1",
"gene_hgnc_id": 11120,
"hgvs_c": "c.1071C>T",
"hgvs_p": "p.Ala357Ala",
"transcript": "ENST00000342245.9",
"protein_id": "ENSP00000340409.4",
"transcript_support_level": 1,
"aa_start": 357,
"aa_end": null,
"aa_length": 631,
"cds_start": 1071,
"cds_end": null,
"cds_length": 1896,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000543.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000342245.9"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPD1",
"gene_hgnc_id": 11120,
"hgvs_c": "c.258C>T",
"hgvs_p": "p.Ala86Ala",
"transcript": "ENST00000526280.1",
"protein_id": "ENSP00000436278.1",
"transcript_support_level": 1,
"aa_start": 86,
"aa_end": null,
"aa_length": 316,
"cds_start": 258,
"cds_end": null,
"cds_length": 951,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000526280.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPD1",
"gene_hgnc_id": 11120,
"hgvs_c": "n.1071C>T",
"hgvs_p": null,
"transcript": "ENST00000533123.5",
"protein_id": "ENSP00000435950.1",
"transcript_support_level": 1,
"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": "ENST00000533123.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPD1",
"gene_hgnc_id": 11120,
"hgvs_c": "n.1071C>T",
"hgvs_p": null,
"transcript": "ENST00000534405.5",
"protein_id": "ENSP00000434353.1",
"transcript_support_level": 1,
"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": "ENST00000534405.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SMPD1",
"gene_hgnc_id": 11120,
"hgvs_c": "n.438+633C>T",
"hgvs_p": null,
"transcript": "ENST00000531303.5",
"protein_id": "ENSP00000432625.1",
"transcript_support_level": 1,
"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": "ENST00000531303.5"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPD1",
"gene_hgnc_id": 11120,
"hgvs_c": "c.110C>T",
"hgvs_p": "p.Pro37Leu",
"transcript": "NM_001318088.2",
"protein_id": "NP_001305017.1",
"transcript_support_level": null,
"aa_start": 37,
"aa_end": null,
"aa_length": 324,
"cds_start": 110,
"cds_end": null,
"cds_length": 975,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001318088.2"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPD1",
"gene_hgnc_id": 11120,
"hgvs_c": "c.1068C>T",
"hgvs_p": "p.Ala356Ala",
"transcript": "NM_001007593.3",
"protein_id": "NP_001007594.2",
"transcript_support_level": null,
"aa_start": 356,
"aa_end": null,
"aa_length": 630,
"cds_start": 1068,
"cds_end": null,
"cds_length": 1893,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001007593.3"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPD1",
"gene_hgnc_id": 11120,
"hgvs_c": "c.1068C>T",
"hgvs_p": "p.Ala356Ala",
"transcript": "ENST00000527275.5",
"protein_id": "ENSP00000435350.1",
"transcript_support_level": 2,
"aa_start": 356,
"aa_end": null,
"aa_length": 630,
"cds_start": 1068,
"cds_end": null,
"cds_length": 1893,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000527275.5"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPD1",
"gene_hgnc_id": 11120,
"hgvs_c": "c.1071C>T",
"hgvs_p": "p.Ala357Ala",
"transcript": "ENST00000880909.1",
"protein_id": "ENSP00000550968.1",
"transcript_support_level": null,
"aa_start": 357,
"aa_end": null,
"aa_length": 624,
"cds_start": 1071,
"cds_end": null,
"cds_length": 1875,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000880909.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPD1",
"gene_hgnc_id": 11120,
"hgvs_c": "c.1071C>T",
"hgvs_p": "p.Ala357Ala",
"transcript": "ENST00000880910.1",
"protein_id": "ENSP00000550969.1",
"transcript_support_level": null,
"aa_start": 357,
"aa_end": null,
"aa_length": 618,
"cds_start": 1071,
"cds_end": null,
"cds_length": 1857,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000880910.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPD1",
"gene_hgnc_id": 11120,
"hgvs_c": "c.1071C>T",
"hgvs_p": "p.Ala357Ala",
"transcript": "NM_001365135.2",
"protein_id": "NP_001352064.1",
"transcript_support_level": null,
"aa_start": 357,
"aa_end": null,
"aa_length": 587,
"cds_start": 1071,
"cds_end": null,
"cds_length": 1764,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001365135.2"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPD1",
"gene_hgnc_id": 11120,
"hgvs_c": "c.1071C>T",
"hgvs_p": "p.Ala357Ala",
"transcript": "NM_001318087.2",
"protein_id": "NP_001305016.1",
"transcript_support_level": null,
"aa_start": 357,
"aa_end": null,
"aa_length": 508,
"cds_start": 1071,
"cds_end": null,
"cds_length": 1527,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001318087.2"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPD1",
"gene_hgnc_id": 11120,
"hgvs_c": "c.1071C>T",
"hgvs_p": "p.Ala357Ala",
"transcript": "XM_011520304.3",
"protein_id": "XP_011518606.1",
"transcript_support_level": null,
"aa_start": 357,
"aa_end": null,
"aa_length": 464,
"cds_start": 1071,
"cds_end": null,
"cds_length": 1395,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011520304.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SMPD1",
"gene_hgnc_id": 11120,
"hgvs_c": "c.951+120C>T",
"hgvs_p": null,
"transcript": "ENST00000880911.1",
"protein_id": "ENSP00000550970.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 527,
"cds_start": null,
"cds_end": null,
"cds_length": 1584,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000880911.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPD1",
"gene_hgnc_id": 11120,
"hgvs_c": "n.1196C>T",
"hgvs_p": null,
"transcript": "NR_027400.3",
"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_027400.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SMPD1",
"gene_hgnc_id": 11120,
"hgvs_c": "n.563+633C>T",
"hgvs_p": null,
"transcript": "NR_134502.2",
"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_134502.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPD1",
"gene_hgnc_id": 11120,
"hgvs_c": "c.*94C>T",
"hgvs_p": null,
"transcript": "ENST00000530395.1",
"protein_id": "ENSP00000431479.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 51,
"cds_start": null,
"cds_end": null,
"cds_length": 158,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000530395.1"
},
{
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPD1",
"gene_hgnc_id": 11120,
"hgvs_c": "n.*80C>T",
"hgvs_p": null,
"transcript": "ENST00000533196.1",
"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": "ENST00000533196.1"
}
],
"gene_symbol": "SMPD1",
"gene_hgnc_id": 11120,
"dbsnp": "rs72896268",
"frequency_reference_population": 0.0075645684,
"hom_count_reference_population": 53,
"allele_count_reference_population": 12210,
"gnomad_exomes_af": 0.00776741,
"gnomad_genomes_af": 0.00561665,
"gnomad_exomes_ac": 11355,
"gnomad_genomes_ac": 855,
"gnomad_exomes_homalt": 50,
"gnomad_genomes_homalt": 3,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.02800000086426735,
"computational_prediction_selected": "Benign",
"computational_source_selected": "REVEL",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.028,
"revel_prediction": "Benign",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.59,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.296,
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "PM1,BP4_Moderate,BP6_Very_Strong,BS2",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 14,
"pathogenic_score": 2,
"criteria": [
"PM1",
"BP4_Moderate",
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_001318088.2",
"gene_symbol": "SMPD1",
"hgnc_id": 11120,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.110C>T",
"hgvs_p": "p.Pro37Leu"
}
],
"clinvar_disease": " type A, type B,Inborn genetic diseases,Niemann-Pick disease,Sphingomyelin/cholesterol lipidosis,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:6 B:5",
"phenotype_combined": "not specified|Niemann-Pick disease, type A|Sphingomyelin/cholesterol lipidosis|not provided|Niemann-Pick disease, type A;Niemann-Pick disease, type B|Inborn genetic diseases",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}