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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: 9-135503570-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=135503570&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PS3",
"PM1",
"PM2",
"PP3_Moderate",
"PP5_Very_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "MRPS2",
"hgnc_id": 14495,
"hgvs_c": "c.328C>T",
"hgvs_p": "p.Arg110Cys",
"inheritance_mode": "Unknown,AR",
"pathogenic_score": 18,
"score": 18,
"transcript": "NM_016034.5",
"verdict": "Pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PS3",
"PM2",
"PP3_Moderate",
"PP5_Very_Strong"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "ENSG00000226706",
"hgnc_id": null,
"hgvs_c": "n.820G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 16,
"score": 16,
"transcript": "ENST00000415062.1",
"verdict": "Pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PS3",
"PM2",
"PP3_Moderate",
"PP5_Very_Strong"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "LOC101928525",
"hgnc_id": null,
"hgvs_c": "n.820G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 16,
"score": 16,
"transcript": "NR_121579.1",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS3,PM1,PM2,PP3_Moderate,PP5_Very_Strong",
"acmg_score": 18,
"allele_count_reference_population": 41,
"alphamissense_prediction": null,
"alphamissense_score": 0.3948,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.14,
"chr": "9",
"clinvar_classification": "Pathogenic",
"clinvar_disease": "Combined oxidative phosphorylation deficiency 36",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.8723363876342773,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 296,
"aa_ref": "R",
"aa_start": 110,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1458,
"cdna_start": 357,
"cds_end": null,
"cds_length": 891,
"cds_start": 328,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_016034.5",
"gene_hgnc_id": 14495,
"gene_symbol": "MRPS2",
"hgvs_c": "c.328C>T",
"hgvs_p": "p.Arg110Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000241600.10",
"protein_coding": true,
"protein_id": "NP_057118.1",
"strand": true,
"transcript": "NM_016034.5",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 296,
"aa_ref": "R",
"aa_start": 110,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1458,
"cdna_start": 357,
"cds_end": null,
"cds_length": 891,
"cds_start": 328,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000241600.10",
"gene_hgnc_id": 14495,
"gene_symbol": "MRPS2",
"hgvs_c": "c.328C>T",
"hgvs_p": "p.Arg110Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_016034.5",
"protein_coding": true,
"protein_id": "ENSP00000241600.5",
"strand": true,
"transcript": "ENST00000241600.10",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1117,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000415062.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000226706",
"hgvs_c": "n.820G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000415062.1",
"transcript_support_level": 1
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 296,
"aa_ref": "R",
"aa_start": 110,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1659,
"cdna_start": 556,
"cds_end": null,
"cds_length": 891,
"cds_start": 328,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_001371401.1",
"gene_hgnc_id": 14495,
"gene_symbol": "MRPS2",
"hgvs_c": "c.328C>T",
"hgvs_p": "p.Arg110Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001358330.1",
"strand": true,
"transcript": "NM_001371401.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 296,
"aa_ref": "R",
"aa_start": 110,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1640,
"cdna_start": 537,
"cds_end": null,
"cds_length": 891,
"cds_start": 328,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000371785.5",
"gene_hgnc_id": 14495,
"gene_symbol": "MRPS2",
"hgvs_c": "c.328C>T",
"hgvs_p": "p.Arg110Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000360850.1",
"strand": true,
"transcript": "ENST00000371785.5",
"transcript_support_level": 3
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 254,
"aa_ref": "R",
"aa_start": 68,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1331,
"cdna_start": 228,
"cds_end": null,
"cds_length": 765,
"cds_start": 202,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000958536.1",
"gene_hgnc_id": 14495,
"gene_symbol": "MRPS2",
"hgvs_c": "c.202C>T",
"hgvs_p": "p.Arg68Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000628595.1",
"strand": true,
"transcript": "ENST00000958536.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 810,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000453385.1",
"gene_hgnc_id": 14495,
"gene_symbol": "MRPS2",
"hgvs_c": "n.370C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000453385.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1714,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000462948.6",
"gene_hgnc_id": 14495,
"gene_symbol": "MRPS2",
"hgvs_c": "n.*201C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000511903.1",
"strand": true,
"transcript": "ENST00000462948.6",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1656,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000472852.2",
"gene_hgnc_id": 14495,
"gene_symbol": "MRPS2",
"hgvs_c": "n.*134C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000511904.1",
"strand": true,
"transcript": "ENST00000472852.2",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 509,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000472946.2",
"gene_hgnc_id": 14495,
"gene_symbol": "MRPS2",
"hgvs_c": "n.93C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000472946.2",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1654,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000485333.6",
"gene_hgnc_id": 14495,
"gene_symbol": "MRPS2",
"hgvs_c": "n.*159C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000511905.1",
"strand": true,
"transcript": "ENST00000485333.6",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1709,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000488610.6",
"gene_hgnc_id": 14495,
"gene_symbol": "MRPS2",
"hgvs_c": "n.*217C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000511906.1",
"strand": true,
"transcript": "ENST00000488610.6",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1603,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NR_051967.3",
"gene_hgnc_id": 14495,
"gene_symbol": "MRPS2",
"hgvs_c": "n.500C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "NR_051967.3",
"transcript_support_level": null
},
{
"aa_alt": null,
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"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1658,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NR_051968.2",
"gene_hgnc_id": 14495,
"gene_symbol": "MRPS2",
"hgvs_c": "n.555C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "NR_051968.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1663,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NR_051969.2",
"gene_hgnc_id": 14495,
"gene_symbol": "MRPS2",
"hgvs_c": "n.560C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "NR_051969.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1605,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NR_051970.2",
"gene_hgnc_id": 14495,
"gene_symbol": "MRPS2",
"hgvs_c": "n.502C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "NR_051970.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1117,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NR_121579.1",
"gene_hgnc_id": null,
"gene_symbol": "LOC101928525",
"hgvs_c": "n.820G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_121579.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1714,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000462948.6",
"gene_hgnc_id": 14495,
"gene_symbol": "MRPS2",
"hgvs_c": "n.*201C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000511903.1",
"strand": true,
"transcript": "ENST00000462948.6",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1656,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000472852.2",
"gene_hgnc_id": 14495,
"gene_symbol": "MRPS2",
"hgvs_c": "n.*134C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000511904.1",
"strand": true,
"transcript": "ENST00000472852.2",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1654,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000485333.6",
"gene_hgnc_id": 14495,
"gene_symbol": "MRPS2",
"hgvs_c": "n.*159C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000511905.1",
"strand": true,
"transcript": "ENST00000485333.6",
"transcript_support_level": 2
},
{
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"aa_end": null,
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],
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"feature": "ENST00000488610.6",
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"protein_id": "ENSP00000511906.1",
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}
],
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"pathogenicity_classification_combined": "Pathogenic",
"phenotype_combined": "Combined oxidative phosphorylation deficiency 36",
"phylop100way_prediction": "Uncertain_significance",
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"ref": "C",
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"splice_prediction_selected": "Benign",
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"splice_source_selected": "max_spliceai",
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}
]
}