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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: 2-216415269-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=216415269&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 216415269,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000357276.9",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMARCAL1",
"gene_hgnc_id": 11102,
"hgvs_c": "c.565A>G",
"hgvs_p": "p.Lys189Glu",
"transcript": "NM_014140.4",
"protein_id": "NP_054859.2",
"transcript_support_level": null,
"aa_start": 189,
"aa_end": null,
"aa_length": 954,
"cds_start": 565,
"cds_end": null,
"cds_length": 2865,
"cdna_start": 825,
"cdna_end": null,
"cdna_length": 3201,
"mane_select": "ENST00000357276.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMARCAL1",
"gene_hgnc_id": 11102,
"hgvs_c": "c.565A>G",
"hgvs_p": "p.Lys189Glu",
"transcript": "ENST00000357276.9",
"protein_id": "ENSP00000349823.4",
"transcript_support_level": 2,
"aa_start": 189,
"aa_end": null,
"aa_length": 954,
"cds_start": 565,
"cds_end": null,
"cds_length": 2865,
"cdna_start": 825,
"cdna_end": null,
"cdna_length": 3201,
"mane_select": "NM_014140.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMARCAL1",
"gene_hgnc_id": 11102,
"hgvs_c": "c.565A>G",
"hgvs_p": "p.Lys189Glu",
"transcript": "ENST00000358207.9",
"protein_id": "ENSP00000350940.5",
"transcript_support_level": 1,
"aa_start": 189,
"aa_end": null,
"aa_length": 954,
"cds_start": 565,
"cds_end": null,
"cds_length": 2865,
"cdna_start": 716,
"cdna_end": null,
"cdna_length": 3056,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMARCAL1",
"gene_hgnc_id": 11102,
"hgvs_c": "c.157A>G",
"hgvs_p": "p.Lys53Glu",
"transcript": "ENST00000392128.6",
"protein_id": "ENSP00000375974.2",
"transcript_support_level": 1,
"aa_start": 53,
"aa_end": null,
"aa_length": 796,
"cds_start": 157,
"cds_end": null,
"cds_length": 2391,
"cdna_start": 157,
"cdna_end": null,
"cdna_length": 2431,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMARCAL1",
"gene_hgnc_id": 11102,
"hgvs_c": "c.565A>G",
"hgvs_p": "p.Lys189Glu",
"transcript": "NM_001127207.2",
"protein_id": "NP_001120679.1",
"transcript_support_level": null,
"aa_start": 189,
"aa_end": null,
"aa_length": 954,
"cds_start": 565,
"cds_end": null,
"cds_length": 2865,
"cdna_start": 694,
"cdna_end": null,
"cdna_length": 3070,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMARCAL1",
"gene_hgnc_id": 11102,
"hgvs_c": "c.565A>G",
"hgvs_p": "p.Lys189Glu",
"transcript": "ENST00000425815.6",
"protein_id": "ENSP00000394410.2",
"transcript_support_level": 3,
"aa_start": 189,
"aa_end": null,
"aa_length": 954,
"cds_start": 565,
"cds_end": null,
"cds_length": 2865,
"cdna_start": 817,
"cdna_end": null,
"cdna_length": 3176,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMARCAL1",
"gene_hgnc_id": 11102,
"hgvs_c": "c.565A>G",
"hgvs_p": "p.Lys189Glu",
"transcript": "ENST00000430374.6",
"protein_id": "ENSP00000405077.2",
"transcript_support_level": 2,
"aa_start": 189,
"aa_end": null,
"aa_length": 954,
"cds_start": 565,
"cds_end": null,
"cds_length": 2865,
"cdna_start": 850,
"cdna_end": null,
"cdna_length": 3210,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMARCAL1",
"gene_hgnc_id": 11102,
"hgvs_c": "c.565A>G",
"hgvs_p": "p.Lys189Glu",
"transcript": "ENST00000444508.6",
"protein_id": "ENSP00000398969.2",
"transcript_support_level": 2,
"aa_start": 189,
"aa_end": null,
"aa_length": 954,
"cds_start": 565,
"cds_end": null,
"cds_length": 2865,
"cdna_start": 885,
"cdna_end": null,
"cdna_length": 3244,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMARCAL1",
"gene_hgnc_id": 11102,
"hgvs_c": "c.565A>G",
"hgvs_p": "p.Lys189Glu",
"transcript": "ENST00000697899.1",
"protein_id": "ENSP00000513470.1",
"transcript_support_level": null,
"aa_start": 189,
"aa_end": null,
"aa_length": 876,
"cds_start": 565,
"cds_end": null,
"cds_length": 2631,
"cdna_start": 850,
"cdna_end": null,
"cdna_length": 2977,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMARCAL1",
"gene_hgnc_id": 11102,
"hgvs_c": "c.565A>G",
"hgvs_p": "p.Lys189Glu",
"transcript": "ENST00000697906.1",
"protein_id": "ENSP00000513475.1",
"transcript_support_level": null,
"aa_start": 189,
"aa_end": null,
"aa_length": 876,
"cds_start": 565,
"cds_end": null,
"cds_length": 2631,
"cdna_start": 709,
"cdna_end": null,
"cdna_length": 2826,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMARCAL1",
"gene_hgnc_id": 11102,
"hgvs_c": "c.262A>G",
"hgvs_p": "p.Lys88Glu",
"transcript": "ENST00000427645.5",
"protein_id": "ENSP00000392997.1",
"transcript_support_level": 3,
"aa_start": 88,
"aa_end": null,
"aa_length": 324,
"cds_start": 262,
"cds_end": null,
"cds_length": 977,
"cdna_start": 262,
"cdna_end": null,
"cdna_length": 977,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMARCAL1",
"gene_hgnc_id": 11102,
"hgvs_c": "n.926A>G",
"hgvs_p": null,
"transcript": "ENST00000697898.1",
"protein_id": null,
"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": 3700,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMARCAL1",
"gene_hgnc_id": 11102,
"hgvs_c": "n.841A>G",
"hgvs_p": null,
"transcript": "ENST00000697900.1",
"protein_id": null,
"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": 3198,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMARCAL1",
"gene_hgnc_id": 11102,
"hgvs_c": "n.565A>G",
"hgvs_p": null,
"transcript": "ENST00000697901.1",
"protein_id": "ENSP00000513471.1",
"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": 3028,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMARCAL1",
"gene_hgnc_id": 11102,
"hgvs_c": "n.797A>G",
"hgvs_p": null,
"transcript": "ENST00000697902.1",
"protein_id": null,
"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": 3173,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMARCAL1",
"gene_hgnc_id": 11102,
"hgvs_c": "n.565A>G",
"hgvs_p": null,
"transcript": "ENST00000697903.1",
"protein_id": "ENSP00000513472.1",
"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": 3002,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMARCAL1",
"gene_hgnc_id": 11102,
"hgvs_c": "n.565A>G",
"hgvs_p": null,
"transcript": "ENST00000697904.1",
"protein_id": "ENSP00000513473.1",
"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": 2926,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMARCAL1",
"gene_hgnc_id": 11102,
"hgvs_c": "n.565A>G",
"hgvs_p": null,
"transcript": "ENST00000697905.1",
"protein_id": "ENSP00000513474.1",
"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": 2962,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMARCAL1",
"gene_hgnc_id": 11102,
"hgvs_c": "n.565A>G",
"hgvs_p": null,
"transcript": "ENST00000697907.1",
"protein_id": "ENSP00000513476.1",
"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": 3054,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SMARCAL1",
"gene_hgnc_id": 11102,
"dbsnp": "rs754147208",
"frequency_reference_population": 0.0000013680994,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 0.0000013681,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.044953495264053345,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.17,
"revel_prediction": "Benign",
"alphamissense_score": 0.0584,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.39,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.159,
"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,BP6",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 5,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "ENST00000357276.9",
"gene_symbol": "SMARCAL1",
"hgnc_id": 11102,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.565A>G",
"hgvs_p": "p.Lys189Glu"
}
],
"clinvar_disease": "Inborn genetic diseases,Schimke immuno-osseous dysplasia",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1",
"phenotype_combined": "Schimke immuno-osseous dysplasia|Inborn genetic diseases",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}