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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: 2-105089924-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=105089924&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 105089924,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_182640.3",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPS9",
"gene_hgnc_id": 14501,
"hgvs_c": "c.580G>A",
"hgvs_p": "p.Val194Met",
"transcript": "NM_182640.3",
"protein_id": "NP_872578.1",
"transcript_support_level": null,
"aa_start": 194,
"aa_end": null,
"aa_length": 396,
"cds_start": 580,
"cds_end": null,
"cds_length": 1191,
"cdna_start": 604,
"cdna_end": null,
"cdna_length": 1414,
"mane_select": "ENST00000258455.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_182640.3"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPS9",
"gene_hgnc_id": 14501,
"hgvs_c": "c.580G>A",
"hgvs_p": "p.Val194Met",
"transcript": "ENST00000258455.8",
"protein_id": "ENSP00000258455.3",
"transcript_support_level": 1,
"aa_start": 194,
"aa_end": null,
"aa_length": 396,
"cds_start": 580,
"cds_end": null,
"cds_length": 1191,
"cdna_start": 604,
"cdna_end": null,
"cdna_length": 1414,
"mane_select": "NM_182640.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000258455.8"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPS9",
"gene_hgnc_id": 14501,
"hgvs_c": "c.580G>A",
"hgvs_p": "p.Val194Met",
"transcript": "ENST00000886286.1",
"protein_id": "ENSP00000556345.1",
"transcript_support_level": null,
"aa_start": 194,
"aa_end": null,
"aa_length": 403,
"cds_start": 580,
"cds_end": null,
"cds_length": 1212,
"cdna_start": 604,
"cdna_end": null,
"cdna_length": 1434,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000886286.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPS9",
"gene_hgnc_id": 14501,
"hgvs_c": "c.580G>A",
"hgvs_p": "p.Val194Met",
"transcript": "ENST00000925255.1",
"protein_id": "ENSP00000595314.1",
"transcript_support_level": null,
"aa_start": 194,
"aa_end": null,
"aa_length": 396,
"cds_start": 580,
"cds_end": null,
"cds_length": 1191,
"cdna_start": 633,
"cdna_end": null,
"cdna_length": 1443,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000925255.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPS9",
"gene_hgnc_id": 14501,
"hgvs_c": "c.580G>A",
"hgvs_p": "p.Val194Met",
"transcript": "ENST00000925256.1",
"protein_id": "ENSP00000595315.1",
"transcript_support_level": null,
"aa_start": 194,
"aa_end": null,
"aa_length": 393,
"cds_start": 580,
"cds_end": null,
"cds_length": 1182,
"cdna_start": 631,
"cdna_end": null,
"cdna_length": 1432,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000925256.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPS9",
"gene_hgnc_id": 14501,
"hgvs_c": "c.517G>A",
"hgvs_p": "p.Val173Met",
"transcript": "ENST00000925257.1",
"protein_id": "ENSP00000595316.1",
"transcript_support_level": null,
"aa_start": 173,
"aa_end": null,
"aa_length": 375,
"cds_start": 517,
"cds_end": null,
"cds_length": 1128,
"cdna_start": 556,
"cdna_end": null,
"cdna_length": 1355,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000925257.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPS9",
"gene_hgnc_id": 14501,
"hgvs_c": "c.487G>A",
"hgvs_p": "p.Val163Met",
"transcript": "ENST00000886284.1",
"protein_id": "ENSP00000556343.1",
"transcript_support_level": null,
"aa_start": 163,
"aa_end": null,
"aa_length": 365,
"cds_start": 487,
"cds_end": null,
"cds_length": 1098,
"cdna_start": 555,
"cdna_end": null,
"cdna_length": 1351,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000886284.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPS9",
"gene_hgnc_id": 14501,
"hgvs_c": "c.484G>A",
"hgvs_p": "p.Val162Met",
"transcript": "ENST00000886285.1",
"protein_id": "ENSP00000556344.1",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 364,
"cds_start": 484,
"cds_end": null,
"cds_length": 1095,
"cdna_start": 508,
"cdna_end": null,
"cdna_length": 1317,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000886285.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPS9",
"gene_hgnc_id": 14501,
"hgvs_c": "c.406G>A",
"hgvs_p": "p.Val136Met",
"transcript": "ENST00000925259.1",
"protein_id": "ENSP00000595318.1",
"transcript_support_level": null,
"aa_start": 136,
"aa_end": null,
"aa_length": 345,
"cds_start": 406,
"cds_end": null,
"cds_length": 1038,
"cdna_start": 414,
"cdna_end": null,
"cdna_length": 1244,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000925259.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPS9",
"gene_hgnc_id": 14501,
"hgvs_c": "c.406G>A",
"hgvs_p": "p.Val136Met",
"transcript": "ENST00000886287.1",
"protein_id": "ENSP00000556346.1",
"transcript_support_level": null,
"aa_start": 136,
"aa_end": null,
"aa_length": 338,
"cds_start": 406,
"cds_end": null,
"cds_length": 1017,
"cdna_start": 430,
"cdna_end": null,
"cdna_length": 1239,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000886287.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPS9",
"gene_hgnc_id": 14501,
"hgvs_c": "c.400G>A",
"hgvs_p": "p.Val134Met",
"transcript": "ENST00000886288.1",
"protein_id": "ENSP00000556347.1",
"transcript_support_level": null,
"aa_start": 134,
"aa_end": null,
"aa_length": 336,
"cds_start": 400,
"cds_end": null,
"cds_length": 1011,
"cdna_start": 424,
"cdna_end": null,
"cdna_length": 1199,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000886288.1"
},
{
"aa_ref": "V",
"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": "MRPS9",
"gene_hgnc_id": 14501,
"hgvs_c": "c.226G>A",
"hgvs_p": "p.Val76Met",
"transcript": "ENST00000925258.1",
"protein_id": "ENSP00000595317.1",
"transcript_support_level": null,
"aa_start": 76,
"aa_end": null,
"aa_length": 278,
"cds_start": 226,
"cds_end": null,
"cds_length": 837,
"cdna_start": 250,
"cdna_end": null,
"cdna_length": 1049,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000925258.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPS9",
"gene_hgnc_id": 14501,
"hgvs_c": "c.208G>A",
"hgvs_p": "p.Val70Met",
"transcript": "XM_011511644.3",
"protein_id": "XP_011509946.1",
"transcript_support_level": null,
"aa_start": 70,
"aa_end": null,
"aa_length": 272,
"cds_start": 208,
"cds_end": null,
"cds_length": 819,
"cdna_start": 412,
"cdna_end": null,
"cdna_length": 1222,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011511644.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPS9",
"gene_hgnc_id": 14501,
"hgvs_c": "c.*483G>A",
"hgvs_p": null,
"transcript": "XM_047445533.1",
"protein_id": "XP_047301489.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 201,
"cds_start": null,
"cds_end": null,
"cds_length": 606,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1163,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047445533.1"
},
{
"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": 9,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "MRPS9",
"gene_hgnc_id": 14501,
"hgvs_c": "c.490-2477G>A",
"hgvs_p": null,
"transcript": "ENST00000886289.1",
"protein_id": "ENSP00000556348.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 342,
"cds_start": null,
"cds_end": null,
"cds_length": 1029,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1202,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000886289.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPS9",
"gene_hgnc_id": 14501,
"hgvs_c": "n.55G>A",
"hgvs_p": null,
"transcript": "ENST00000413583.5",
"protein_id": "ENSP00000388885.1",
"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": 652,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000413583.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "MRPS9-AS1",
"gene_hgnc_id": 40688,
"hgvs_c": "n.433-6457C>T",
"hgvs_p": null,
"transcript": "ENST00000791480.1",
"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": 722,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000791480.1"
}
],
"gene_symbol": "MRPS9",
"gene_hgnc_id": 14501,
"dbsnp": "rs759417452",
"frequency_reference_population": 0.000039856517,
"hom_count_reference_population": 0,
"allele_count_reference_population": 64,
"gnomad_exomes_af": 0.000042652,
"gnomad_genomes_af": 0.0000131461,
"gnomad_exomes_ac": 62,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.08161884546279907,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.232,
"revel_prediction": "Benign",
"alphamissense_score": 0.088,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.19,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.554,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": "BP4_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_182640.3",
"gene_symbol": "MRPS9",
"hgnc_id": 14501,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.580G>A",
"hgvs_p": "p.Val194Met"
},
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000791480.1",
"gene_symbol": "MRPS9-AS1",
"hgnc_id": 40688,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.433-6457C>T",
"hgvs_p": null
}
],
"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
}