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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: X-101412328-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=101412328&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PP2",
"PP3",
"PP5_Very_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "HNRNPH2",
"hgnc_id": 5042,
"hgvs_c": "c.340C>T",
"hgvs_p": "p.Arg114Trp",
"inheritance_mode": "XL",
"pathogenic_score": 12,
"score": 12,
"transcript": "NM_019597.5",
"verdict": "Pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3",
"PP5_Very_Strong"
],
"effects": [
"3_prime_UTR_variant"
],
"gene_symbol": "RPL36A-HNRNPH2",
"hgnc_id": 48349,
"hgvs_c": "c.*336C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 11,
"score": 11,
"transcript": "NM_001199973.2",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PP2,PP3,PP5_Very_Strong",
"acmg_score": 12,
"allele_count_reference_population": 0,
"alphamissense_prediction": "Pathogenic",
"alphamissense_score": 0.9573,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.06,
"chr": "X",
"clinvar_classification": "Pathogenic",
"clinvar_disease": " Bain type, X-linked, syndromic,Intellectual disability,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.7976679801940918,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 449,
"aa_ref": "R",
"aa_start": 114,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2296,
"cdna_start": 491,
"cds_end": null,
"cds_length": 1350,
"cds_start": 340,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_019597.5",
"gene_hgnc_id": 5042,
"gene_symbol": "HNRNPH2",
"hgvs_c": "c.340C>T",
"hgvs_p": "p.Arg114Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000316594.6",
"protein_coding": true,
"protein_id": "NP_062543.1",
"strand": true,
"transcript": "NM_019597.5",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 449,
"aa_ref": "R",
"aa_start": 114,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2296,
"cdna_start": 491,
"cds_end": null,
"cds_length": 1350,
"cds_start": 340,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000316594.6",
"gene_hgnc_id": 5042,
"gene_symbol": "HNRNPH2",
"hgvs_c": "c.340C>T",
"hgvs_p": "p.Arg114Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_019597.5",
"protein_coding": true,
"protein_id": "ENSP00000361927.2",
"strand": true,
"transcript": "ENST00000316594.6",
"transcript_support_level": 1
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 449,
"aa_ref": "R",
"aa_start": 114,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2284,
"cdna_start": 479,
"cds_end": null,
"cds_length": 1350,
"cds_start": 340,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_001032393.3",
"gene_hgnc_id": 5042,
"gene_symbol": "HNRNPH2",
"hgvs_c": "c.340C>T",
"hgvs_p": "p.Arg114Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001027565.1",
"strand": true,
"transcript": "NM_001032393.3",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 449,
"aa_ref": "R",
"aa_start": 114,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2396,
"cdna_start": 587,
"cds_end": null,
"cds_length": 1350,
"cds_start": 340,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000867410.1",
"gene_hgnc_id": 5042,
"gene_symbol": "HNRNPH2",
"hgvs_c": "c.340C>T",
"hgvs_p": "p.Arg114Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000537469.1",
"strand": true,
"transcript": "ENST00000867410.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 449,
"aa_ref": "R",
"aa_start": 114,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2301,
"cdna_start": 496,
"cds_end": null,
"cds_length": 1350,
"cds_start": 340,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000867411.1",
"gene_hgnc_id": 5042,
"gene_symbol": "HNRNPH2",
"hgvs_c": "c.340C>T",
"hgvs_p": "p.Arg114Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000537470.1",
"strand": true,
"transcript": "ENST00000867411.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 449,
"aa_ref": "R",
"aa_start": 114,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2316,
"cdna_start": 511,
"cds_end": null,
"cds_length": 1350,
"cds_start": 340,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000867412.1",
"gene_hgnc_id": 5042,
"gene_symbol": "HNRNPH2",
"hgvs_c": "c.340C>T",
"hgvs_p": "p.Arg114Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000537471.1",
"strand": true,
"transcript": "ENST00000867412.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 449,
"aa_ref": "R",
"aa_start": 114,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2262,
"cdna_start": 457,
"cds_end": null,
"cds_length": 1350,
"cds_start": 340,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000867413.1",
"gene_hgnc_id": 5042,
"gene_symbol": "HNRNPH2",
"hgvs_c": "c.340C>T",
"hgvs_p": "p.Arg114Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000537472.1",
"strand": true,
"transcript": "ENST00000867413.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 449,
"aa_ref": "R",
"aa_start": 114,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2329,
"cdna_start": 524,
"cds_end": null,
"cds_length": 1350,
"cds_start": 340,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000918125.1",
"gene_hgnc_id": 5042,
"gene_symbol": "HNRNPH2",
"hgvs_c": "c.340C>T",
"hgvs_p": "p.Arg114Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000588184.1",
"strand": true,
"transcript": "ENST00000918125.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 449,
"aa_ref": "R",
"aa_start": 114,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2313,
"cdna_start": 515,
"cds_end": null,
"cds_length": 1350,
"cds_start": 340,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000942884.1",
"gene_hgnc_id": 5042,
"gene_symbol": "HNRNPH2",
"hgvs_c": "c.340C>T",
"hgvs_p": "p.Arg114Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000612943.1",
"strand": true,
"transcript": "ENST00000942884.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 449,
"aa_ref": "R",
"aa_start": 114,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2381,
"cdna_start": 583,
"cds_end": null,
"cds_length": 1350,
"cds_start": 340,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000942885.1",
"gene_hgnc_id": 5042,
"gene_symbol": "HNRNPH2",
"hgvs_c": "c.340C>T",
"hgvs_p": "p.Arg114Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000612944.1",
"strand": true,
"transcript": "ENST00000942885.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 449,
"aa_ref": "R",
"aa_start": 114,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2369,
"cdna_start": 572,
"cds_end": null,
"cds_length": 1350,
"cds_start": 340,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000942886.1",
"gene_hgnc_id": 5042,
"gene_symbol": "HNRNPH2",
"hgvs_c": "c.340C>T",
"hgvs_p": "p.Arg114Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000612945.1",
"strand": true,
"transcript": "ENST00000942886.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 449,
"aa_ref": "R",
"aa_start": 114,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2296,
"cdna_start": 491,
"cds_end": null,
"cds_length": 1350,
"cds_start": 340,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000942887.1",
"gene_hgnc_id": 5042,
"gene_symbol": "HNRNPH2",
"hgvs_c": "c.340C>T",
"hgvs_p": "p.Arg114Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000612946.1",
"strand": true,
"transcript": "ENST00000942887.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 118,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2531,
"cdna_start": null,
"cds_end": null,
"cds_length": 357,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_001199973.2",
"gene_hgnc_id": 48349,
"gene_symbol": "RPL36A-HNRNPH2",
"hgvs_c": "c.*336C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001186902.2",
"strand": true,
"transcript": "NM_001199973.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 77,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2408,
"cdna_start": null,
"cds_end": null,
"cds_length": 234,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_001199974.2",
"gene_hgnc_id": 48349,
"gene_symbol": "RPL36A-HNRNPH2",
"hgvs_c": "c.*336C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001186903.2",
"strand": true,
"transcript": "NM_001199974.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 118,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 562,
"cdna_start": null,
"cds_end": null,
"cds_length": 357,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000409170.3",
"gene_hgnc_id": 48349,
"gene_symbol": "RPL36A-HNRNPH2",
"hgvs_c": "c.*336C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000386655.4",
"strand": true,
"transcript": "ENST00000409170.3",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 77,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 572,
"cdna_start": null,
"cds_end": null,
"cds_length": 234,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000409338.5",
"gene_hgnc_id": 48349,
"gene_symbol": "RPL36A-HNRNPH2",
"hgvs_c": "c.*336C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000386974.2",
"strand": true,
"transcript": "ENST00000409338.5",
"transcript_support_level": 4
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs782191163",
"effect": "missense_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 5042,
"gene_symbol": "HNRNPH2",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Pathogenic",
"phenotype_combined": "Intellectual disability, X-linked, syndromic, Bain type|not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": 3.086,
"pos": 101412328,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.275,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_019597.5"
}
]
}