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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: 3-131462789-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=131462789&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 131462789,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "NM_007208.4",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.981A>G",
"hgvs_p": "p.Glu327Glu",
"transcript": "NM_007208.4",
"protein_id": "NP_009139.1",
"transcript_support_level": null,
"aa_start": 327,
"aa_end": null,
"aa_length": 348,
"cds_start": 981,
"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": "E",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.981A>G",
"hgvs_p": "p.Glu327Glu",
"transcript": "ENST00000264995.8",
"protein_id": "ENSP00000264995.2",
"transcript_support_level": 1,
"aa_start": 327,
"aa_end": null,
"aa_length": 348,
"cds_start": 981,
"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": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.1062A>G",
"hgvs_p": "p.Glu354Glu",
"transcript": "ENST00000425847.6",
"protein_id": "ENSP00000398536.2",
"transcript_support_level": 2,
"aa_start": 354,
"aa_end": null,
"aa_length": 375,
"cds_start": 1062,
"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": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.1023A>G",
"hgvs_p": "p.Glu341Glu",
"transcript": "ENST00000511168.5",
"protein_id": "ENSP00000424107.1",
"transcript_support_level": 2,
"aa_start": 341,
"aa_end": null,
"aa_length": 362,
"cds_start": 1023,
"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": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.999A>G",
"hgvs_p": "p.Glu333Glu",
"transcript": "ENST00000908740.1",
"protein_id": "ENSP00000578799.1",
"transcript_support_level": null,
"aa_start": 333,
"aa_end": null,
"aa_length": 354,
"cds_start": 999,
"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": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.957A>G",
"hgvs_p": "p.Glu319Glu",
"transcript": "ENST00000908739.1",
"protein_id": "ENSP00000578798.1",
"transcript_support_level": null,
"aa_start": 319,
"aa_end": null,
"aa_length": 340,
"cds_start": 957,
"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": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.927A>G",
"hgvs_p": "p.Glu309Glu",
"transcript": "ENST00000908741.1",
"protein_id": "ENSP00000578800.1",
"transcript_support_level": null,
"aa_start": 309,
"aa_end": null,
"aa_length": 330,
"cds_start": 927,
"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": "E",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_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.555A>G",
"hgvs_p": "p.Glu185Glu",
"transcript": "ENST00000925018.1",
"protein_id": "ENSP00000595077.1",
"transcript_support_level": null,
"aa_start": 185,
"aa_end": null,
"aa_length": 206,
"cds_start": 555,
"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.405A>G",
"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": "rs780672468",
"frequency_reference_population": 0.0000061992055,
"hom_count_reference_population": 0,
"allele_count_reference_population": 10,
"gnomad_exomes_af": 0.00000547575,
"gnomad_genomes_af": 0.0000131473,
"gnomad_exomes_ac": 8,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.24699999392032623,
"computational_prediction_selected": "Benign",
"computational_source_selected": "REVEL",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.247,
"revel_prediction": "Benign",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.54,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.081,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4,BP6_Moderate,BP7",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4",
"BP6_Moderate",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "NM_007208.4",
"gene_symbol": "MRPL3",
"hgnc_id": 10379,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.981A>G",
"hgvs_p": "p.Glu327Glu"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}