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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: 3-131462785-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=131462785&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 131462785,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_007208.4",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPL3",
"gene_hgnc_id": 10379,
"hgvs_c": "c.985C>T",
"hgvs_p": "p.Pro329Ser",
"transcript": "NM_007208.4",
"protein_id": "NP_009139.1",
"transcript_support_level": null,
"aa_start": 329,
"aa_end": null,
"aa_length": 348,
"cds_start": 985,
"cds_end": null,
"cds_length": 1047,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000264995.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_007208.4"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPL3",
"gene_hgnc_id": 10379,
"hgvs_c": "c.985C>T",
"hgvs_p": "p.Pro329Ser",
"transcript": "ENST00000264995.8",
"protein_id": "ENSP00000264995.2",
"transcript_support_level": 1,
"aa_start": 329,
"aa_end": null,
"aa_length": 348,
"cds_start": 985,
"cds_end": null,
"cds_length": 1047,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_007208.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000264995.8"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPL3",
"gene_hgnc_id": 10379,
"hgvs_c": "c.1066C>T",
"hgvs_p": "p.Pro356Ser",
"transcript": "ENST00000425847.6",
"protein_id": "ENSP00000398536.2",
"transcript_support_level": 2,
"aa_start": 356,
"aa_end": null,
"aa_length": 375,
"cds_start": 1066,
"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": "ENST00000425847.6"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPL3",
"gene_hgnc_id": 10379,
"hgvs_c": "c.1027C>T",
"hgvs_p": "p.Pro343Ser",
"transcript": "ENST00000511168.5",
"protein_id": "ENSP00000424107.1",
"transcript_support_level": 2,
"aa_start": 343,
"aa_end": null,
"aa_length": 362,
"cds_start": 1027,
"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": "ENST00000511168.5"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPL3",
"gene_hgnc_id": 10379,
"hgvs_c": "c.1003C>T",
"hgvs_p": "p.Pro335Ser",
"transcript": "ENST00000908740.1",
"protein_id": "ENSP00000578799.1",
"transcript_support_level": null,
"aa_start": 335,
"aa_end": null,
"aa_length": 354,
"cds_start": 1003,
"cds_end": null,
"cds_length": 1065,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000908740.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPL3",
"gene_hgnc_id": 10379,
"hgvs_c": "c.961C>T",
"hgvs_p": "p.Pro321Ser",
"transcript": "ENST00000908739.1",
"protein_id": "ENSP00000578798.1",
"transcript_support_level": null,
"aa_start": 321,
"aa_end": null,
"aa_length": 340,
"cds_start": 961,
"cds_end": null,
"cds_length": 1023,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000908739.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPL3",
"gene_hgnc_id": 10379,
"hgvs_c": "c.931C>T",
"hgvs_p": "p.Pro311Ser",
"transcript": "ENST00000908741.1",
"protein_id": "ENSP00000578800.1",
"transcript_support_level": null,
"aa_start": 311,
"aa_end": null,
"aa_length": 330,
"cds_start": 931,
"cds_end": null,
"cds_length": 993,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000908741.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPL3",
"gene_hgnc_id": 10379,
"hgvs_c": "c.559C>T",
"hgvs_p": "p.Pro187Ser",
"transcript": "ENST00000925018.1",
"protein_id": "ENSP00000595077.1",
"transcript_support_level": null,
"aa_start": 187,
"aa_end": null,
"aa_length": 206,
"cds_start": 559,
"cds_end": null,
"cds_length": 621,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000925018.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPL3",
"gene_hgnc_id": 10379,
"hgvs_c": "n.409C>T",
"hgvs_p": null,
"transcript": "ENST00000510043.1",
"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": "retained_intron",
"feature": "ENST00000510043.1"
}
],
"gene_symbol": "MRPL3",
"gene_hgnc_id": 10379,
"dbsnp": "rs145183319",
"frequency_reference_population": 0.00016925698,
"hom_count_reference_population": 1,
"allele_count_reference_population": 273,
"gnomad_exomes_af": 0.00016703,
"gnomad_genomes_af": 0.000190641,
"gnomad_exomes_ac": 244,
"gnomad_genomes_ac": 29,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.012918561697006226,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.487,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1377,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.11,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.252,
"phylop100way_prediction": "Uncertain_significance",
"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": "NM_007208.4",
"gene_symbol": "MRPL3",
"hgnc_id": 10379,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.985C>T",
"hgvs_p": "p.Pro329Ser"
}
],
"clinvar_disease": "not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:2 LB:1",
"phenotype_combined": "not provided|not specified",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}