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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: 10-12136142-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=12136142&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 12136142,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_018144.4",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC61A2",
"gene_hgnc_id": 17702,
"hgvs_c": "c.113C>T",
"hgvs_p": "p.Thr38Met",
"transcript": "NM_018144.4",
"protein_id": "NP_060614.2",
"transcript_support_level": null,
"aa_start": 38,
"aa_end": null,
"aa_length": 476,
"cds_start": 113,
"cds_end": null,
"cds_length": 1431,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000298428.14",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_018144.4"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC61A2",
"gene_hgnc_id": 17702,
"hgvs_c": "c.113C>T",
"hgvs_p": "p.Thr38Met",
"transcript": "ENST00000298428.14",
"protein_id": "ENSP00000298428.9",
"transcript_support_level": 1,
"aa_start": 38,
"aa_end": null,
"aa_length": 476,
"cds_start": 113,
"cds_end": null,
"cds_length": 1431,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_018144.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000298428.14"
},
{
"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": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC61A2",
"gene_hgnc_id": 17702,
"hgvs_c": "n.113C>T",
"hgvs_p": null,
"transcript": "ENST00000475268.5",
"protein_id": "ENSP00000436749.1",
"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": "ENST00000475268.5"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC61A2",
"gene_hgnc_id": 17702,
"hgvs_c": "c.113C>T",
"hgvs_p": "p.Thr38Met",
"transcript": "NM_001142627.3",
"protein_id": "NP_001136099.1",
"transcript_support_level": null,
"aa_start": 38,
"aa_end": null,
"aa_length": 437,
"cds_start": 113,
"cds_end": null,
"cds_length": 1314,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001142627.3"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC61A2",
"gene_hgnc_id": 17702,
"hgvs_c": "c.113C>T",
"hgvs_p": "p.Thr38Met",
"transcript": "ENST00000304267.12",
"protein_id": "ENSP00000302048.8",
"transcript_support_level": 2,
"aa_start": 38,
"aa_end": null,
"aa_length": 437,
"cds_start": 113,
"cds_end": null,
"cds_length": 1314,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000304267.12"
},
{
"aa_ref": "T",
"aa_alt": "M",
"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": "SEC61A2",
"gene_hgnc_id": 17702,
"hgvs_c": "c.113C>T",
"hgvs_p": "p.Thr38Met",
"transcript": "ENST00000379020.8",
"protein_id": "ENSP00000368306.3",
"transcript_support_level": 5,
"aa_start": 38,
"aa_end": null,
"aa_length": 410,
"cds_start": 113,
"cds_end": null,
"cds_length": 1233,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000379020.8"
},
{
"aa_ref": "T",
"aa_alt": "M",
"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": "SEC61A2",
"gene_hgnc_id": 17702,
"hgvs_c": "c.113C>T",
"hgvs_p": "p.Thr38Met",
"transcript": "ENST00000905219.1",
"protein_id": "ENSP00000575278.1",
"transcript_support_level": null,
"aa_start": 38,
"aa_end": null,
"aa_length": 344,
"cds_start": 113,
"cds_end": null,
"cds_length": 1035,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000905219.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"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": "SEC61A2",
"gene_hgnc_id": 17702,
"hgvs_c": "c.113C>T",
"hgvs_p": "p.Thr38Met",
"transcript": "ENST00000441368.5",
"protein_id": "ENSP00000404959.1",
"transcript_support_level": 5,
"aa_start": 38,
"aa_end": null,
"aa_length": 188,
"cds_start": 113,
"cds_end": null,
"cds_length": 569,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000441368.5"
},
{
"aa_ref": "T",
"aa_alt": "M",
"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": "SEC61A2",
"gene_hgnc_id": 17702,
"hgvs_c": "c.113C>T",
"hgvs_p": "p.Thr38Met",
"transcript": "ENST00000379017.7",
"protein_id": "ENSP00000368302.3",
"transcript_support_level": 5,
"aa_start": 38,
"aa_end": null,
"aa_length": 168,
"cds_start": 113,
"cds_end": null,
"cds_length": 507,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000379017.7"
},
{
"aa_ref": "T",
"aa_alt": "M",
"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": "SEC61A2",
"gene_hgnc_id": 17702,
"hgvs_c": "c.113C>T",
"hgvs_p": "p.Thr38Met",
"transcript": "ENST00000379051.5",
"protein_id": "ENSP00000368339.1",
"transcript_support_level": 3,
"aa_start": 38,
"aa_end": null,
"aa_length": 159,
"cds_start": 113,
"cds_end": null,
"cds_length": 480,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000379051.5"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC61A2",
"gene_hgnc_id": 17702,
"hgvs_c": "c.32C>T",
"hgvs_p": "p.Thr11Met",
"transcript": "ENST00000457034.1",
"protein_id": "ENSP00000401731.1",
"transcript_support_level": 5,
"aa_start": 11,
"aa_end": null,
"aa_length": 93,
"cds_start": 32,
"cds_end": null,
"cds_length": 282,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000457034.1"
},
{
"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": 11,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SEC61A2",
"gene_hgnc_id": 17702,
"hgvs_c": "c.75+2834C>T",
"hgvs_p": null,
"transcript": "NM_001142628.1",
"protein_id": "NP_001136100.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 454,
"cds_start": null,
"cds_end": null,
"cds_length": 1365,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001142628.1"
},
{
"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": 11,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SEC61A2",
"gene_hgnc_id": 17702,
"hgvs_c": "c.75+2834C>T",
"hgvs_p": null,
"transcript": "ENST00000379033.7",
"protein_id": "ENSP00000368319.3",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 454,
"cds_start": null,
"cds_end": null,
"cds_length": 1365,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000379033.7"
},
{
"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": "SEC61A2",
"gene_hgnc_id": 17702,
"hgvs_c": "n.113C>T",
"hgvs_p": null,
"transcript": "ENST00000472221.5",
"protein_id": "ENSP00000436294.1",
"transcript_support_level": 2,
"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": "ENST00000472221.5"
},
{
"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": "SEC61A2",
"gene_hgnc_id": 17702,
"hgvs_c": "n.202C>T",
"hgvs_p": null,
"transcript": "ENST00000495368.1",
"protein_id": null,
"transcript_support_level": 2,
"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": "ENST00000495368.1"
},
{
"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": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEC61A2",
"gene_hgnc_id": 17702,
"hgvs_c": "n.224C>T",
"hgvs_p": null,
"transcript": "NR_024576.3",
"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_024576.3"
},
{
"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": "SEC61A2",
"gene_hgnc_id": 17702,
"hgvs_c": "n.224C>T",
"hgvs_p": null,
"transcript": "NR_024577.3",
"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_024577.3"
}
],
"gene_symbol": "SEC61A2",
"gene_hgnc_id": 17702,
"dbsnp": "rs2131645940",
"frequency_reference_population": 6.9012253e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.90123e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7011086940765381,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.05000000074505806,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.304,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.8173,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.22,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.459,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.05,
"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": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_018144.4",
"gene_symbol": "SEC61A2",
"hgnc_id": 17702,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.113C>T",
"hgvs_p": "p.Thr38Met"
}
],
"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
}