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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: 5-178150934-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=178150934&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [],
"effects": [
"missense_variant"
],
"gene_symbol": "NHP2",
"hgnc_id": 14377,
"hgvs_c": "c.290T>C",
"hgvs_p": "p.Met97Thr",
"inheritance_mode": "AR,AD",
"pathogenic_score": 0,
"score": 0,
"transcript": "NM_001396110.1",
"verdict": "Uncertain_significance"
},
{
"benign_score": 0,
"criteria": [],
"effects": [
"3_prime_UTR_variant"
],
"gene_symbol": "RMND5B",
"hgnc_id": 26181,
"hgvs_c": "c.*2902A>G",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": 0,
"transcript": "ENST00000890008.1",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "",
"acmg_score": 0,
"allele_count_reference_population": 209,
"alphamissense_prediction": null,
"alphamissense_score": 0.7499,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.17,
"chr": "5",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Dyskeratosis congenita",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.6487590074539185,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 153,
"aa_ref": "M",
"aa_start": 97,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 780,
"cdna_start": 358,
"cds_end": null,
"cds_length": 462,
"cds_start": 290,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_017838.4",
"gene_hgnc_id": 14377,
"gene_symbol": "NHP2",
"hgvs_c": "c.290T>C",
"hgvs_p": "p.Met97Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000274606.8",
"protein_coding": true,
"protein_id": "NP_060308.1",
"strand": false,
"transcript": "NM_017838.4",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 153,
"aa_ref": "M",
"aa_start": 97,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 780,
"cdna_start": 358,
"cds_end": null,
"cds_length": 462,
"cds_start": 290,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000274606.8",
"gene_hgnc_id": 14377,
"gene_symbol": "NHP2",
"hgvs_c": "c.290T>C",
"hgvs_p": "p.Met97Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_017838.4",
"protein_coding": true,
"protein_id": "ENSP00000274606.4",
"strand": false,
"transcript": "ENST00000274606.8",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 168,
"aa_ref": "M",
"aa_start": 97,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 908,
"cdna_start": 358,
"cds_end": null,
"cds_length": 507,
"cds_start": 290,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_001396110.1",
"gene_hgnc_id": 14377,
"gene_symbol": "NHP2",
"hgvs_c": "c.290T>C",
"hgvs_p": "p.Met97Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001383039.1",
"strand": false,
"transcript": "NM_001396110.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 159,
"aa_ref": "M",
"aa_start": 103,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 874,
"cdna_start": 452,
"cds_end": null,
"cds_length": 480,
"cds_start": 308,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000940843.1",
"gene_hgnc_id": 14377,
"gene_symbol": "NHP2",
"hgvs_c": "c.308T>C",
"hgvs_p": "p.Met103Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000610902.1",
"strand": false,
"transcript": "ENST00000940843.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 134,
"aa_ref": "M",
"aa_start": 97,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 472,
"cdna_start": 355,
"cds_end": null,
"cds_length": 407,
"cds_start": 290,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000514354.5",
"gene_hgnc_id": 14377,
"gene_symbol": "NHP2",
"hgvs_c": "c.290T>C",
"hgvs_p": "p.Met97Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000423803.1",
"strand": false,
"transcript": "ENST00000514354.5",
"transcript_support_level": 3
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 131,
"aa_ref": "M",
"aa_start": 97,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 475,
"cdna_start": 367,
"cds_end": null,
"cds_length": 398,
"cds_start": 290,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000511078.1",
"gene_hgnc_id": 14377,
"gene_symbol": "NHP2",
"hgvs_c": "c.290T>C",
"hgvs_p": "p.Met97Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000423849.1",
"strand": false,
"transcript": "ENST00000511078.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 393,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5791,
"cdna_start": null,
"cds_end": null,
"cds_length": 1182,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000890008.1",
"gene_hgnc_id": 26181,
"gene_symbol": "RMND5B",
"hgvs_c": "c.*2902A>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000560067.1",
"strand": true,
"transcript": "ENST00000890008.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 130,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 710,
"cdna_start": null,
"cds_end": null,
"cds_length": 393,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000890268.1",
"gene_hgnc_id": 14377,
"gene_symbol": "NHP2",
"hgvs_c": "c.267+23T>C",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000560327.1",
"strand": false,
"transcript": "ENST00000890268.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 114,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 697,
"cdna_start": null,
"cds_end": null,
"cds_length": 345,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000940844.1",
"gene_hgnc_id": 14377,
"gene_symbol": "NHP2",
"hgvs_c": "c.220-1096T>C",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000610903.1",
"strand": false,
"transcript": "ENST00000940844.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 90,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 674,
"cdna_start": null,
"cds_end": null,
"cds_length": 273,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001034833.2",
"gene_hgnc_id": 14377,
"gene_symbol": "NHP2",
"hgvs_c": "c.231-1096T>C",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001030005.1",
"strand": false,
"transcript": "NM_001034833.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 90,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 637,
"cdna_start": null,
"cds_end": null,
"cds_length": 273,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000314397.9",
"gene_hgnc_id": 14377,
"gene_symbol": "NHP2",
"hgvs_c": "c.231-1096T>C",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000366276.2",
"strand": false,
"transcript": "ENST00000314397.9",
"transcript_support_level": 2
},
{
"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": 552,
"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": "ENST00000502263.1",
"gene_hgnc_id": 14377,
"gene_symbol": "NHP2",
"hgvs_c": "n.149T>C",
"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": "ENST00000502263.1",
"transcript_support_level": 2
},
{
"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": 613,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000697323.1",
"gene_hgnc_id": 14377,
"gene_symbol": "NHP2",
"hgvs_c": "n.191T>C",
"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": "ENST00000697323.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs147530082",
"effect": "missense_variant",
"frequency_reference_population": 0.00012950494,
"gene_hgnc_id": 14377,
"gene_symbol": "NHP2",
"gnomad_exomes_ac": 201,
"gnomad_exomes_af": 0.000137512,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_ac": 8,
"gnomad_genomes_af": 0.0000525804,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 1,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "Dyskeratosis congenita",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 9.265,
"pos": 178150934,
"ref": "A",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.533,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001396110.1"
}
]
}