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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: 6-31753314-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=31753314&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 31753314,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_172165.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "c.826C>T",
"hgvs_p": "p.Arg276Cys",
"transcript": "NM_172166.4",
"protein_id": "NP_751898.1",
"transcript_support_level": null,
"aa_start": 276,
"aa_end": null,
"aa_length": 834,
"cds_start": 826,
"cds_end": null,
"cds_length": 2505,
"cdna_start": 897,
"cdna_end": null,
"cdna_length": 2721,
"mane_select": "ENST00000375750.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_172166.4"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "c.826C>T",
"hgvs_p": "p.Arg276Cys",
"transcript": "ENST00000375750.9",
"protein_id": "ENSP00000364903.3",
"transcript_support_level": 1,
"aa_start": 276,
"aa_end": null,
"aa_length": 834,
"cds_start": 826,
"cds_end": null,
"cds_length": 2505,
"cdna_start": 897,
"cdna_end": null,
"cdna_length": 2721,
"mane_select": "NM_172166.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000375750.9"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "c.826C>T",
"hgvs_p": "p.Arg276Cys",
"transcript": "ENST00000375703.7",
"protein_id": "ENSP00000364855.3",
"transcript_support_level": 1,
"aa_start": 276,
"aa_end": null,
"aa_length": 835,
"cds_start": 826,
"cds_end": null,
"cds_length": 2508,
"cdna_start": 881,
"cdna_end": null,
"cdna_length": 2708,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000375703.7"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "c.826C>T",
"hgvs_p": "p.Arg276Cys",
"transcript": "ENST00000375755.8",
"protein_id": "ENSP00000364908.3",
"transcript_support_level": 1,
"aa_start": 276,
"aa_end": null,
"aa_length": 834,
"cds_start": 826,
"cds_end": null,
"cds_length": 2505,
"cdna_start": 1112,
"cdna_end": null,
"cdna_length": 2936,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000375755.8"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "c.877C>T",
"hgvs_p": "p.Arg293Cys",
"transcript": "ENST00000375740.7",
"protein_id": "ENSP00000364892.3",
"transcript_support_level": 1,
"aa_start": 293,
"aa_end": null,
"aa_length": 822,
"cds_start": 877,
"cds_end": null,
"cds_length": 2469,
"cdna_start": 932,
"cdna_end": null,
"cdna_length": 2669,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000375740.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH5-SAPCD1",
"gene_hgnc_id": 41994,
"hgvs_c": "n.877C>T",
"hgvs_p": null,
"transcript": "ENST00000493662.6",
"protein_id": "ENSP00000417871.2",
"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": 3991,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000493662.6"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "c.826C>T",
"hgvs_p": "p.Arg276Cys",
"transcript": "NM_172165.4",
"protein_id": "NP_751897.1",
"transcript_support_level": null,
"aa_start": 276,
"aa_end": null,
"aa_length": 835,
"cds_start": 826,
"cds_end": null,
"cds_length": 2508,
"cdna_start": 897,
"cdna_end": null,
"cdna_length": 2724,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_172165.4"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "c.826C>T",
"hgvs_p": "p.Arg276Cys",
"transcript": "NM_002441.5",
"protein_id": "NP_002432.1",
"transcript_support_level": null,
"aa_start": 276,
"aa_end": null,
"aa_length": 834,
"cds_start": 826,
"cds_end": null,
"cds_length": 2505,
"cdna_start": 1055,
"cdna_end": null,
"cdna_length": 2879,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002441.5"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "c.877C>T",
"hgvs_p": "p.Arg293Cys",
"transcript": "NM_025259.6",
"protein_id": "NP_079535.4",
"transcript_support_level": null,
"aa_start": 293,
"aa_end": null,
"aa_length": 822,
"cds_start": 877,
"cds_end": null,
"cds_length": 2469,
"cdna_start": 948,
"cdna_end": null,
"cdna_length": 2685,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_025259.6"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "c.337C>T",
"hgvs_p": "p.Arg113Cys",
"transcript": "ENST00000450148.5",
"protein_id": "ENSP00000394971.1",
"transcript_support_level": 5,
"aa_start": 113,
"aa_end": null,
"aa_length": 332,
"cds_start": 337,
"cds_end": null,
"cds_length": 1000,
"cdna_start": 337,
"cdna_end": null,
"cdna_length": 1000,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000450148.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "n.826C>T",
"hgvs_p": null,
"transcript": "ENST00000423982.6",
"protein_id": "ENSP00000406352.2",
"transcript_support_level": 5,
"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": 2706,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000423982.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "n.*35C>T",
"hgvs_p": null,
"transcript": "ENST00000463144.5",
"protein_id": "ENSP00000419648.1",
"transcript_support_level": 5,
"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": 2296,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000463144.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "n.32C>T",
"hgvs_p": null,
"transcript": "ENST00000468136.5",
"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": 690,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000468136.5"
},
{
"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": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "n.172C>T",
"hgvs_p": null,
"transcript": "ENST00000468602.5",
"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": 637,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000468602.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "n.*35C>T",
"hgvs_p": null,
"transcript": "ENST00000497269.5",
"protein_id": "ENSP00000419131.1",
"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": 764,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000497269.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH5-SAPCD1",
"gene_hgnc_id": 41994,
"hgvs_c": "n.1005C>T",
"hgvs_p": null,
"transcript": "NR_037846.1",
"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": 4063,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_037846.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "n.*35C>T",
"hgvs_p": null,
"transcript": "ENST00000463144.5",
"protein_id": "ENSP00000419648.1",
"transcript_support_level": 5,
"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": 2296,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000463144.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "n.*35C>T",
"hgvs_p": null,
"transcript": "ENST00000497269.5",
"protein_id": "ENSP00000419131.1",
"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": 764,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000497269.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "n.1118-4851C>T",
"hgvs_p": null,
"transcript": "ENST00000650702.1",
"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": 3053,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000650702.1"
}
],
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"dbsnp": "rs144471639",
"frequency_reference_population": 0.0000049633886,
"hom_count_reference_population": 0,
"allele_count_reference_population": 8,
"gnomad_exomes_af": 0.00000479574,
"gnomad_genomes_af": 0.00000657142,
"gnomad_exomes_ac": 7,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8839308619499207,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.1599999964237213,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.804,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.2697,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.4,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 2.164,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.16,
"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": 5,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate,PP5",
"acmg_by_gene": [
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "NM_172165.4",
"gene_symbol": "MSH5",
"hgnc_id": 7328,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,Unknown",
"hgvs_c": "c.826C>T",
"hgvs_p": "p.Arg276Cys"
},
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000493662.6",
"gene_symbol": "MSH5-SAPCD1",
"hgnc_id": 41994,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.877C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Genetic non-acquired premature ovarian failure",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Genetic non-acquired premature ovarian failure",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}