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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: X-53381028-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=53381028&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 53381028,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_006306.4",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC1A",
"gene_hgnc_id": 11111,
"hgvs_c": "c.3497A>G",
"hgvs_p": "p.Asn1166Ser",
"transcript": "NM_006306.4",
"protein_id": "NP_006297.2",
"transcript_support_level": null,
"aa_start": 1166,
"aa_end": null,
"aa_length": 1233,
"cds_start": 3497,
"cds_end": null,
"cds_length": 3702,
"cdna_start": 3551,
"cdna_end": null,
"cdna_length": 9710,
"mane_select": "ENST00000322213.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006306.4"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC1A",
"gene_hgnc_id": 11111,
"hgvs_c": "c.3497A>G",
"hgvs_p": "p.Asn1166Ser",
"transcript": "ENST00000322213.9",
"protein_id": "ENSP00000323421.3",
"transcript_support_level": 1,
"aa_start": 1166,
"aa_end": null,
"aa_length": 1233,
"cds_start": 3497,
"cds_end": null,
"cds_length": 3702,
"cdna_start": 3551,
"cdna_end": null,
"cdna_length": 9710,
"mane_select": "NM_006306.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000322213.9"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC1A",
"gene_hgnc_id": 11111,
"hgvs_c": "c.3431A>G",
"hgvs_p": "p.Asn1144Ser",
"transcript": "ENST00000375340.10",
"protein_id": "ENSP00000364489.7",
"transcript_support_level": 1,
"aa_start": 1144,
"aa_end": null,
"aa_length": 1211,
"cds_start": 3431,
"cds_end": null,
"cds_length": 3636,
"cdna_start": 3771,
"cdna_end": null,
"cdna_length": 9930,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000375340.10"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC1A",
"gene_hgnc_id": 11111,
"hgvs_c": "c.3431A>G",
"hgvs_p": "p.Asn1144Ser",
"transcript": "NM_001281463.1",
"protein_id": "NP_001268392.1",
"transcript_support_level": null,
"aa_start": 1144,
"aa_end": null,
"aa_length": 1211,
"cds_start": 3431,
"cds_end": null,
"cds_length": 3636,
"cdna_start": 3771,
"cdna_end": null,
"cdna_length": 9930,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001281463.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC1A",
"gene_hgnc_id": 11111,
"hgvs_c": "c.3431A>G",
"hgvs_p": "p.Asn1144Ser",
"transcript": "ENST00000675504.1",
"protein_id": "ENSP00000502524.1",
"transcript_support_level": null,
"aa_start": 1144,
"aa_end": null,
"aa_length": 1211,
"cds_start": 3431,
"cds_end": null,
"cds_length": 3636,
"cdna_start": 3667,
"cdna_end": null,
"cdna_length": 9826,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000675504.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC1A",
"gene_hgnc_id": 11111,
"hgvs_c": "c.3131A>G",
"hgvs_p": "p.Asn1044Ser",
"transcript": "ENST00000947776.1",
"protein_id": "ENSP00000617835.1",
"transcript_support_level": null,
"aa_start": 1044,
"aa_end": null,
"aa_length": 1111,
"cds_start": 3131,
"cds_end": null,
"cds_length": 3336,
"cdna_start": 3208,
"cdna_end": null,
"cdna_length": 5540,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000947776.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC1A",
"gene_hgnc_id": 11111,
"hgvs_c": "c.2795A>G",
"hgvs_p": "p.Asn932Ser",
"transcript": "ENST00000947777.1",
"protein_id": "ENSP00000617836.1",
"transcript_support_level": null,
"aa_start": 932,
"aa_end": null,
"aa_length": 999,
"cds_start": 2795,
"cds_end": null,
"cds_length": 3000,
"cdna_start": 2882,
"cdna_end": null,
"cdna_length": 4734,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000947777.1"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC1A",
"gene_hgnc_id": 11111,
"hgvs_c": "c.2729A>G",
"hgvs_p": "p.Asn910Ser",
"transcript": "ENST00000674590.1",
"protein_id": "ENSP00000502626.1",
"transcript_support_level": null,
"aa_start": 910,
"aa_end": null,
"aa_length": 977,
"cds_start": 2729,
"cds_end": null,
"cds_length": 2934,
"cdna_start": 3069,
"cdna_end": null,
"cdna_length": 3323,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000674590.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SMC1A",
"gene_hgnc_id": 11111,
"hgvs_c": "c.726-298A>G",
"hgvs_p": null,
"transcript": "ENST00000470241.2",
"protein_id": "ENSP00000476416.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 277,
"cds_start": null,
"cds_end": null,
"cds_length": 836,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 838,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000470241.2"
}
],
"gene_symbol": "SMC1A",
"gene_hgnc_id": 11111,
"dbsnp": "rs1556885810",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9807093143463135,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.772,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9814,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.21,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.986,
"phylop100way_prediction": "Pathogenic",
"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": 9,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PM5,PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 9,
"benign_score": 0,
"pathogenic_score": 9,
"criteria": [
"PM2",
"PM5",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_006306.4",
"gene_symbol": "SMC1A",
"hgnc_id": 11111,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL,AD",
"hgvs_c": "c.3497A>G",
"hgvs_p": "p.Asn1166Ser"
}
],
"clinvar_disease": "Congenital muscular hypertrophy-cerebral syndrome,Inborn genetic diseases",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:2 US:1",
"phenotype_combined": "Inborn genetic diseases|Congenital muscular hypertrophy-cerebral syndrome",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}