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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: 5-178149799-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=178149799&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 178149799,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000274606.8",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NHP2",
"gene_hgnc_id": 14377,
"hgvs_c": "c.376G>A",
"hgvs_p": "p.Val126Met",
"transcript": "NM_017838.4",
"protein_id": "NP_060308.1",
"transcript_support_level": null,
"aa_start": 126,
"aa_end": null,
"aa_length": 153,
"cds_start": 376,
"cds_end": null,
"cds_length": 462,
"cdna_start": 444,
"cdna_end": null,
"cdna_length": 780,
"mane_select": "ENST00000274606.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NHP2",
"gene_hgnc_id": 14377,
"hgvs_c": "c.376G>A",
"hgvs_p": "p.Val126Met",
"transcript": "ENST00000274606.8",
"protein_id": "ENSP00000274606.4",
"transcript_support_level": 1,
"aa_start": 126,
"aa_end": null,
"aa_length": 153,
"cds_start": 376,
"cds_end": null,
"cds_length": 462,
"cdna_start": 444,
"cdna_end": null,
"cdna_length": 780,
"mane_select": "NM_017838.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RMND5B",
"gene_hgnc_id": 26181,
"hgvs_c": "c.*1767C>T",
"hgvs_p": null,
"transcript": "NM_022762.5",
"protein_id": "NP_073599.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 393,
"cds_start": -4,
"cds_end": null,
"cds_length": 1182,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3911,
"mane_select": "ENST00000313386.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RMND5B",
"gene_hgnc_id": 26181,
"hgvs_c": "c.*1767C>T",
"hgvs_p": null,
"transcript": "ENST00000313386.9",
"protein_id": "ENSP00000320623.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 393,
"cds_start": -4,
"cds_end": null,
"cds_length": 1182,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3911,
"mane_select": "NM_022762.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NHP2",
"gene_hgnc_id": 14377,
"hgvs_c": "c.504G>A",
"hgvs_p": "p.Val168Val",
"transcript": "NM_001396110.1",
"protein_id": "NP_001383039.1",
"transcript_support_level": null,
"aa_start": 168,
"aa_end": null,
"aa_length": 168,
"cds_start": 504,
"cds_end": null,
"cds_length": 507,
"cdna_start": 572,
"cdna_end": null,
"cdna_length": 908,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NHP2",
"gene_hgnc_id": 14377,
"hgvs_c": "c.270G>A",
"hgvs_p": "p.Val90Val",
"transcript": "NM_001034833.2",
"protein_id": "NP_001030005.1",
"transcript_support_level": null,
"aa_start": 90,
"aa_end": null,
"aa_length": 90,
"cds_start": 270,
"cds_end": null,
"cds_length": 273,
"cdna_start": 338,
"cdna_end": null,
"cdna_length": 674,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NHP2",
"gene_hgnc_id": 14377,
"hgvs_c": "c.270G>A",
"hgvs_p": "p.Val90Val",
"transcript": "ENST00000314397.9",
"protein_id": "ENSP00000366276.2",
"transcript_support_level": 2,
"aa_start": 90,
"aa_end": null,
"aa_length": 90,
"cds_start": 270,
"cds_end": null,
"cds_length": 273,
"cdna_start": 301,
"cdna_end": null,
"cdna_length": 637,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RMND5B",
"gene_hgnc_id": 26181,
"hgvs_c": "n.4058C>T",
"hgvs_p": null,
"transcript": "ENST00000513162.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4250,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NHP2",
"gene_hgnc_id": 14377,
"hgvs_c": "n.277G>A",
"hgvs_p": null,
"transcript": "ENST00000697323.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 613,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RMND5B",
"gene_hgnc_id": 26181,
"hgvs_c": "c.*1767C>T",
"hgvs_p": null,
"transcript": "NM_001288794.2",
"protein_id": "NP_001275723.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 393,
"cds_start": -4,
"cds_end": null,
"cds_length": 1182,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4051,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RMND5B",
"gene_hgnc_id": 26181,
"hgvs_c": "c.*1767C>T",
"hgvs_p": null,
"transcript": "ENST00000515098.5",
"protein_id": "ENSP00000420875.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 393,
"cds_start": -4,
"cds_end": null,
"cds_length": 1182,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4066,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RMND5B",
"gene_hgnc_id": 26181,
"hgvs_c": "c.*1767C>T",
"hgvs_p": null,
"transcript": "NM_001288795.2",
"protein_id": "NP_001275724.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 380,
"cds_start": -4,
"cds_end": null,
"cds_length": 1143,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3900,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RMND5B",
"gene_hgnc_id": 26181,
"hgvs_c": "c.*1767C>T",
"hgvs_p": null,
"transcript": "XM_005265969.5",
"protein_id": "XP_005266026.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 393,
"cds_start": -4,
"cds_end": null,
"cds_length": 1182,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3771,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RMND5B",
"gene_hgnc_id": 26181,
"hgvs_c": "c.*1767C>T",
"hgvs_p": null,
"transcript": "XM_047417525.1",
"protein_id": "XP_047273481.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 393,
"cds_start": -4,
"cds_end": null,
"cds_length": 1182,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4093,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RMND5B",
"gene_hgnc_id": 26181,
"hgvs_c": "c.*1767C>T",
"hgvs_p": null,
"transcript": "XM_047417526.1",
"protein_id": "XP_047273482.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 393,
"cds_start": -4,
"cds_end": null,
"cds_length": 1182,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3873,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RMND5B",
"gene_hgnc_id": 26181,
"hgvs_c": "c.*1767C>T",
"hgvs_p": null,
"transcript": "XM_005265972.4",
"protein_id": "XP_005266029.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 333,
"cds_start": -4,
"cds_end": null,
"cds_length": 1002,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3693,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RMND5B",
"gene_hgnc_id": 26181,
"hgvs_c": "c.*1767C>T",
"hgvs_p": null,
"transcript": "XM_017009728.2",
"protein_id": "XP_016865217.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 333,
"cds_start": -4,
"cds_end": null,
"cds_length": 1002,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3760,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NHP2",
"gene_hgnc_id": 14377,
"dbsnp": "rs121908090",
"frequency_reference_population": 6.841405e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84141e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9479732513427734,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.382,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9103,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.18,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.828,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0,
"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": 7,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000274606.8",
"gene_symbol": "NHP2",
"hgnc_id": 14377,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.376G>A",
"hgvs_p": "p.Val126Met"
},
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000313386.9",
"gene_symbol": "RMND5B",
"hgnc_id": 26181,
"effects": [
"3_prime_UTR_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.*1767C>T",
"hgvs_p": null
}
],
"clinvar_disease": " autosomal recessive 1, autosomal recessive 2,Dyskeratosis congenita",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "O:1",
"phenotype_combined": "Dyskeratosis congenita, autosomal recessive 2|Dyskeratosis congenita, autosomal recessive 1",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}