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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-53382605-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=53382605&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 53382605,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_006306.4",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC1A",
"gene_hgnc_id": 11111,
"hgvs_c": "c.3186C>G",
"hgvs_p": "p.Ile1062Met",
"transcript": "NM_006306.4",
"protein_id": "NP_006297.2",
"transcript_support_level": null,
"aa_start": 1062,
"aa_end": null,
"aa_length": 1233,
"cds_start": 3186,
"cds_end": null,
"cds_length": 3702,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000322213.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006306.4"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC1A",
"gene_hgnc_id": 11111,
"hgvs_c": "c.3186C>G",
"hgvs_p": "p.Ile1062Met",
"transcript": "ENST00000322213.9",
"protein_id": "ENSP00000323421.3",
"transcript_support_level": 1,
"aa_start": 1062,
"aa_end": null,
"aa_length": 1233,
"cds_start": 3186,
"cds_end": null,
"cds_length": 3702,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_006306.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000322213.9"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC1A",
"gene_hgnc_id": 11111,
"hgvs_c": "c.3120C>G",
"hgvs_p": "p.Ile1040Met",
"transcript": "ENST00000375340.10",
"protein_id": "ENSP00000364489.7",
"transcript_support_level": 1,
"aa_start": 1040,
"aa_end": null,
"aa_length": 1211,
"cds_start": 3120,
"cds_end": null,
"cds_length": 3636,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000375340.10"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC1A",
"gene_hgnc_id": 11111,
"hgvs_c": "c.3120C>G",
"hgvs_p": "p.Ile1040Met",
"transcript": "NM_001281463.1",
"protein_id": "NP_001268392.1",
"transcript_support_level": null,
"aa_start": 1040,
"aa_end": null,
"aa_length": 1211,
"cds_start": 3120,
"cds_end": null,
"cds_length": 3636,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001281463.1"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC1A",
"gene_hgnc_id": 11111,
"hgvs_c": "c.3120C>G",
"hgvs_p": "p.Ile1040Met",
"transcript": "ENST00000675504.1",
"protein_id": "ENSP00000502524.1",
"transcript_support_level": null,
"aa_start": 1040,
"aa_end": null,
"aa_length": 1211,
"cds_start": 3120,
"cds_end": null,
"cds_length": 3636,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000675504.1"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC1A",
"gene_hgnc_id": 11111,
"hgvs_c": "c.2820C>G",
"hgvs_p": "p.Ile940Met",
"transcript": "ENST00000947776.1",
"protein_id": "ENSP00000617835.1",
"transcript_support_level": null,
"aa_start": 940,
"aa_end": null,
"aa_length": 1111,
"cds_start": 2820,
"cds_end": null,
"cds_length": 3336,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000947776.1"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC1A",
"gene_hgnc_id": 11111,
"hgvs_c": "c.2484C>G",
"hgvs_p": "p.Ile828Met",
"transcript": "ENST00000947777.1",
"protein_id": "ENSP00000617836.1",
"transcript_support_level": null,
"aa_start": 828,
"aa_end": null,
"aa_length": 999,
"cds_start": 2484,
"cds_end": null,
"cds_length": 3000,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000947777.1"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC1A",
"gene_hgnc_id": 11111,
"hgvs_c": "c.2418C>G",
"hgvs_p": "p.Ile806Met",
"transcript": "ENST00000674590.1",
"protein_id": "ENSP00000502626.1",
"transcript_support_level": null,
"aa_start": 806,
"aa_end": null,
"aa_length": 977,
"cds_start": 2418,
"cds_end": null,
"cds_length": 2934,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000674590.1"
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC1A",
"gene_hgnc_id": 11111,
"hgvs_c": "c.474C>G",
"hgvs_p": "p.Ile158Met",
"transcript": "ENST00000470241.2",
"protein_id": "ENSP00000476416.1",
"transcript_support_level": 3,
"aa_start": 158,
"aa_end": null,
"aa_length": 277,
"cds_start": 474,
"cds_end": null,
"cds_length": 836,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000470241.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMC1A",
"gene_hgnc_id": 11111,
"hgvs_c": "n.42C>G",
"hgvs_p": null,
"transcript": "ENST00000469129.1",
"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": "retained_intron",
"feature": "ENST00000469129.1"
}
],
"gene_symbol": "SMC1A",
"gene_hgnc_id": 11111,
"dbsnp": "rs372307204",
"frequency_reference_population": 0.00009918978,
"hom_count_reference_population": 33,
"allele_count_reference_population": 120,
"gnomad_exomes_af": 0.000105644,
"gnomad_genomes_af": 0.0000357849,
"gnomad_exomes_ac": 116,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.36859047412872314,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.448,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1206,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.22,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.428,
"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": -7,
"acmg_classification": "Benign",
"acmg_criteria": "PM1,BP4,BS1,BS2",
"acmg_by_gene": [
{
"score": -7,
"benign_score": 9,
"pathogenic_score": 2,
"criteria": [
"PM1",
"BP4",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_006306.4",
"gene_symbol": "SMC1A",
"hgnc_id": 11111,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL,AD",
"hgvs_c": "c.3186C>G",
"hgvs_p": "p.Ile1062Met"
}
],
"clinvar_disease": " 85, with or without midline brain defects,Congenital muscular hypertrophy-cerebral syndrome,Developmental and epileptic encephalopathy,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:4",
"phenotype_combined": "Developmental and epileptic encephalopathy, 85, with or without midline brain defects;Congenital muscular hypertrophy-cerebral syndrome|Congenital muscular hypertrophy-cerebral syndrome|not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}