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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: 6-31744238-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=31744238&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 31744238,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_172165.4",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "c.586G>C",
"hgvs_p": "p.Gly196Arg",
"transcript": "NM_172166.4",
"protein_id": "NP_751898.1",
"transcript_support_level": null,
"aa_start": 196,
"aa_end": null,
"aa_length": 834,
"cds_start": 586,
"cds_end": null,
"cds_length": 2505,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000375750.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_172166.4"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "c.586G>C",
"hgvs_p": "p.Gly196Arg",
"transcript": "ENST00000375750.9",
"protein_id": "ENSP00000364903.3",
"transcript_support_level": 1,
"aa_start": 196,
"aa_end": null,
"aa_length": 834,
"cds_start": 586,
"cds_end": null,
"cds_length": 2505,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_172166.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000375750.9"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "c.586G>C",
"hgvs_p": "p.Gly196Arg",
"transcript": "ENST00000375703.7",
"protein_id": "ENSP00000364855.3",
"transcript_support_level": 1,
"aa_start": 196,
"aa_end": null,
"aa_length": 835,
"cds_start": 586,
"cds_end": null,
"cds_length": 2508,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000375703.7"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "c.586G>C",
"hgvs_p": "p.Gly196Arg",
"transcript": "ENST00000375755.8",
"protein_id": "ENSP00000364908.3",
"transcript_support_level": 1,
"aa_start": 196,
"aa_end": null,
"aa_length": 834,
"cds_start": 586,
"cds_end": null,
"cds_length": 2505,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000375755.8"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "c.637G>C",
"hgvs_p": "p.Gly213Arg",
"transcript": "ENST00000375740.7",
"protein_id": "ENSP00000364892.3",
"transcript_support_level": 1,
"aa_start": 213,
"aa_end": null,
"aa_length": 822,
"cds_start": 637,
"cds_end": null,
"cds_length": 2469,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"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": 7,
"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.637G>C",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000493662.6"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "c.586G>C",
"hgvs_p": "p.Gly196Arg",
"transcript": "NM_172165.4",
"protein_id": "NP_751897.1",
"transcript_support_level": null,
"aa_start": 196,
"aa_end": null,
"aa_length": 835,
"cds_start": 586,
"cds_end": null,
"cds_length": 2508,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_172165.4"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "c.586G>C",
"hgvs_p": "p.Gly196Arg",
"transcript": "NM_002441.5",
"protein_id": "NP_002432.1",
"transcript_support_level": null,
"aa_start": 196,
"aa_end": null,
"aa_length": 834,
"cds_start": 586,
"cds_end": null,
"cds_length": 2505,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002441.5"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "c.637G>C",
"hgvs_p": "p.Gly213Arg",
"transcript": "NM_025259.6",
"protein_id": "NP_079535.4",
"transcript_support_level": null,
"aa_start": 213,
"aa_end": null,
"aa_length": 822,
"cds_start": 637,
"cds_end": null,
"cds_length": 2469,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_025259.6"
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "c.97G>C",
"hgvs_p": "p.Gly33Arg",
"transcript": "ENST00000450148.5",
"protein_id": "ENSP00000394971.1",
"transcript_support_level": 5,
"aa_start": 33,
"aa_end": null,
"aa_length": 332,
"cds_start": 97,
"cds_end": null,
"cds_length": 1000,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"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": 6,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "n.586G>C",
"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": null,
"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": 5,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "n.355G>C",
"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": null,
"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": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "n.657G>C",
"hgvs_p": null,
"transcript": "ENST00000482280.1",
"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": "ENST00000482280.1"
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "n.7G>C",
"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": null,
"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": 6,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "n.974G>C",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000650702.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"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.765G>C",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_037846.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"hgvs_c": "c.*4G>C",
"hgvs_p": null,
"transcript": "ENST00000425703.5",
"protein_id": "ENSP00000402842.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 193,
"cds_start": null,
"cds_end": null,
"cds_length": 582,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000425703.5"
}
],
"gene_symbol": "MSH5",
"gene_hgnc_id": 7328,
"dbsnp": "rs375514940",
"frequency_reference_population": 0.0000030979434,
"hom_count_reference_population": 0,
"allele_count_reference_population": 5,
"gnomad_exomes_af": 0.00000205223,
"gnomad_genomes_af": 0.0000131453,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.768502950668335,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.609,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.8385,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.22,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 4.016,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.02,
"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": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "NM_172165.4",
"gene_symbol": "MSH5",
"hgnc_id": 7328,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,Unknown",
"hgvs_c": "c.586G>C",
"hgvs_p": "p.Gly196Arg"
},
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000493662.6",
"gene_symbol": "MSH5-SAPCD1",
"hgnc_id": 41994,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.637G>C",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}