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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: 2-88087872-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=88087872&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 88087872,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_198274.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMYD1",
"gene_hgnc_id": 20986,
"hgvs_c": "c.325C>T",
"hgvs_p": "p.Arg109Cys",
"transcript": "NM_198274.4",
"protein_id": "NP_938015.1",
"transcript_support_level": null,
"aa_start": 109,
"aa_end": null,
"aa_length": 490,
"cds_start": 325,
"cds_end": null,
"cds_length": 1473,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000419482.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_198274.4"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMYD1",
"gene_hgnc_id": 20986,
"hgvs_c": "c.325C>T",
"hgvs_p": "p.Arg109Cys",
"transcript": "ENST00000419482.7",
"protein_id": "ENSP00000393453.2",
"transcript_support_level": 1,
"aa_start": 109,
"aa_end": null,
"aa_length": 490,
"cds_start": 325,
"cds_end": null,
"cds_length": 1473,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_198274.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000419482.7"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMYD1",
"gene_hgnc_id": 20986,
"hgvs_c": "c.325C>T",
"hgvs_p": "p.Arg109Cys",
"transcript": "ENST00000965777.1",
"protein_id": "ENSP00000635836.1",
"transcript_support_level": null,
"aa_start": 109,
"aa_end": null,
"aa_length": 524,
"cds_start": 325,
"cds_end": null,
"cds_length": 1575,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000965777.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMYD1",
"gene_hgnc_id": 20986,
"hgvs_c": "c.421C>T",
"hgvs_p": "p.Arg141Cys",
"transcript": "ENST00000965776.1",
"protein_id": "ENSP00000635835.1",
"transcript_support_level": null,
"aa_start": 141,
"aa_end": null,
"aa_length": 522,
"cds_start": 421,
"cds_end": null,
"cds_length": 1569,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000965776.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMYD1",
"gene_hgnc_id": 20986,
"hgvs_c": "c.325C>T",
"hgvs_p": "p.Arg109Cys",
"transcript": "ENST00000965774.1",
"protein_id": "ENSP00000635833.1",
"transcript_support_level": null,
"aa_start": 109,
"aa_end": null,
"aa_length": 511,
"cds_start": 325,
"cds_end": null,
"cds_length": 1536,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000965774.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMYD1",
"gene_hgnc_id": 20986,
"hgvs_c": "c.325C>T",
"hgvs_p": "p.Arg109Cys",
"transcript": "ENST00000891942.1",
"protein_id": "ENSP00000562001.1",
"transcript_support_level": null,
"aa_start": 109,
"aa_end": null,
"aa_length": 487,
"cds_start": 325,
"cds_end": null,
"cds_length": 1464,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000891942.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMYD1",
"gene_hgnc_id": 20986,
"hgvs_c": "c.325C>T",
"hgvs_p": "p.Arg109Cys",
"transcript": "ENST00000965779.1",
"protein_id": "ENSP00000635838.1",
"transcript_support_level": null,
"aa_start": 109,
"aa_end": null,
"aa_length": 484,
"cds_start": 325,
"cds_end": null,
"cds_length": 1455,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000965779.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMYD1",
"gene_hgnc_id": 20986,
"hgvs_c": "c.325C>T",
"hgvs_p": "p.Arg109Cys",
"transcript": "NM_001330364.2",
"protein_id": "NP_001317293.1",
"transcript_support_level": null,
"aa_start": 109,
"aa_end": null,
"aa_length": 477,
"cds_start": 325,
"cds_end": null,
"cds_length": 1434,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001330364.2"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMYD1",
"gene_hgnc_id": 20986,
"hgvs_c": "c.325C>T",
"hgvs_p": "p.Arg109Cys",
"transcript": "ENST00000444564.2",
"protein_id": "ENSP00000407888.2",
"transcript_support_level": 5,
"aa_start": 109,
"aa_end": null,
"aa_length": 477,
"cds_start": 325,
"cds_end": null,
"cds_length": 1434,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000444564.2"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMYD1",
"gene_hgnc_id": 20986,
"hgvs_c": "c.325C>T",
"hgvs_p": "p.Arg109Cys",
"transcript": "ENST00000965778.1",
"protein_id": "ENSP00000635837.1",
"transcript_support_level": null,
"aa_start": 109,
"aa_end": null,
"aa_length": 471,
"cds_start": 325,
"cds_end": null,
"cds_length": 1416,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000965778.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMYD1",
"gene_hgnc_id": 20986,
"hgvs_c": "c.325C>T",
"hgvs_p": "p.Arg109Cys",
"transcript": "ENST00000965780.1",
"protein_id": "ENSP00000635839.1",
"transcript_support_level": null,
"aa_start": 109,
"aa_end": null,
"aa_length": 464,
"cds_start": 325,
"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": "ENST00000965780.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMYD1",
"gene_hgnc_id": 20986,
"hgvs_c": "c.148C>T",
"hgvs_p": "p.Arg50Cys",
"transcript": "ENST00000891941.1",
"protein_id": "ENSP00000562000.1",
"transcript_support_level": null,
"aa_start": 50,
"aa_end": null,
"aa_length": 431,
"cds_start": 148,
"cds_end": null,
"cds_length": 1296,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000891941.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMYD1",
"gene_hgnc_id": 20986,
"hgvs_c": "c.148C>T",
"hgvs_p": "p.Arg50Cys",
"transcript": "ENST00000965773.1",
"protein_id": "ENSP00000635832.1",
"transcript_support_level": null,
"aa_start": 50,
"aa_end": null,
"aa_length": 418,
"cds_start": 148,
"cds_end": null,
"cds_length": 1257,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000965773.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMYD1",
"gene_hgnc_id": 20986,
"hgvs_c": "c.325C>T",
"hgvs_p": "p.Arg109Cys",
"transcript": "ENST00000891943.1",
"protein_id": "ENSP00000562002.1",
"transcript_support_level": null,
"aa_start": 109,
"aa_end": null,
"aa_length": 370,
"cds_start": 325,
"cds_end": null,
"cds_length": 1113,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000891943.1"
},
{
"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": 8,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SMYD1",
"gene_hgnc_id": 20986,
"hgvs_c": "c.314+3380C>T",
"hgvs_p": null,
"transcript": "ENST00000965772.1",
"protein_id": "ENSP00000635831.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 375,
"cds_start": null,
"cds_end": null,
"cds_length": 1128,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000965772.1"
},
{
"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": 7,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SMYD1",
"gene_hgnc_id": 20986,
"hgvs_c": "c.314+3380C>T",
"hgvs_p": null,
"transcript": "ENST00000965775.1",
"protein_id": "ENSP00000635834.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 362,
"cds_start": null,
"cds_end": null,
"cds_length": 1089,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000965775.1"
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SMYD1",
"gene_hgnc_id": 20986,
"hgvs_c": "c.294+3400C>T",
"hgvs_p": null,
"transcript": "ENST00000438570.1",
"protein_id": "ENSP00000387482.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 103,
"cds_start": null,
"cds_end": null,
"cds_length": 312,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000438570.1"
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMYD1",
"gene_hgnc_id": 20986,
"hgvs_c": "n.355C>T",
"hgvs_p": null,
"transcript": "ENST00000468008.1",
"protein_id": null,
"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": "pseudogene",
"feature": "ENST00000468008.1"
}
],
"gene_symbol": "SMYD1",
"gene_hgnc_id": 20986,
"dbsnp": "rs773786522",
"frequency_reference_population": 0.0000041854023,
"hom_count_reference_population": 0,
"allele_count_reference_population": 6,
"gnomad_exomes_af": 0.0000041854,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 6,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9313719272613525,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.556,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.5951,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.13,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 2.819,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP3_Moderate,BS2",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PP3_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_198274.4",
"gene_symbol": "SMYD1",
"hgnc_id": 20986,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.325C>T",
"hgvs_p": "p.Arg109Cys"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}