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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: 14-75106541-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=75106541&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "14",
"pos": 75106541,
"ref": "G",
"alt": "A",
"effect": "stop_gained",
"transcript": "NM_001329237.2",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK9",
"gene_hgnc_id": 18591,
"hgvs_c": "c.1489C>T",
"hgvs_p": "p.Arg497*",
"transcript": "NM_033116.6",
"protein_id": "NP_149107.4",
"transcript_support_level": null,
"aa_start": 497,
"aa_end": null,
"aa_length": 979,
"cds_start": 1489,
"cds_end": null,
"cds_length": 2940,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000238616.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_033116.6"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK9",
"gene_hgnc_id": 18591,
"hgvs_c": "c.1489C>T",
"hgvs_p": "p.Arg497*",
"transcript": "ENST00000238616.10",
"protein_id": "ENSP00000238616.5",
"transcript_support_level": 1,
"aa_start": 497,
"aa_end": null,
"aa_length": 979,
"cds_start": 1489,
"cds_end": null,
"cds_length": 2940,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_033116.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000238616.10"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK9",
"gene_hgnc_id": 18591,
"hgvs_c": "c.1489C>T",
"hgvs_p": "p.Arg497*",
"transcript": "NM_001329237.2",
"protein_id": "NP_001316166.1",
"transcript_support_level": null,
"aa_start": 497,
"aa_end": null,
"aa_length": 991,
"cds_start": 1489,
"cds_end": null,
"cds_length": 2976,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001329237.2"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK9",
"gene_hgnc_id": 18591,
"hgvs_c": "c.1489C>T",
"hgvs_p": "p.Arg497*",
"transcript": "ENST00000678037.1",
"protein_id": "ENSP00000504620.1",
"transcript_support_level": null,
"aa_start": 497,
"aa_end": null,
"aa_length": 991,
"cds_start": 1489,
"cds_end": null,
"cds_length": 2976,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000678037.1"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK9",
"gene_hgnc_id": 18591,
"hgvs_c": "c.1489C>T",
"hgvs_p": "p.Arg497*",
"transcript": "ENST00000909801.1",
"protein_id": "ENSP00000579860.1",
"transcript_support_level": null,
"aa_start": 497,
"aa_end": null,
"aa_length": 981,
"cds_start": 1489,
"cds_end": null,
"cds_length": 2946,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000909801.1"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK9",
"gene_hgnc_id": 18591,
"hgvs_c": "c.1489C>T",
"hgvs_p": "p.Arg497*",
"transcript": "ENST00000909800.1",
"protein_id": "ENSP00000579859.1",
"transcript_support_level": null,
"aa_start": 497,
"aa_end": null,
"aa_length": 959,
"cds_start": 1489,
"cds_end": null,
"cds_length": 2880,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000909800.1"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK9",
"gene_hgnc_id": 18591,
"hgvs_c": "c.1489C>T",
"hgvs_p": "p.Arg497*",
"transcript": "ENST00000944755.1",
"protein_id": "ENSP00000614814.1",
"transcript_support_level": null,
"aa_start": 497,
"aa_end": null,
"aa_length": 959,
"cds_start": 1489,
"cds_end": null,
"cds_length": 2880,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000944755.1"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK9",
"gene_hgnc_id": 18591,
"hgvs_c": "c.1255C>T",
"hgvs_p": "p.Arg419*",
"transcript": "ENST00000909799.1",
"protein_id": "ENSP00000579858.1",
"transcript_support_level": null,
"aa_start": 419,
"aa_end": null,
"aa_length": 901,
"cds_start": 1255,
"cds_end": null,
"cds_length": 2706,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000909799.1"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK9",
"gene_hgnc_id": 18591,
"hgvs_c": "c.1135C>T",
"hgvs_p": "p.Arg379*",
"transcript": "NM_001329238.2",
"protein_id": "NP_001316167.1",
"transcript_support_level": null,
"aa_start": 379,
"aa_end": null,
"aa_length": 861,
"cds_start": 1135,
"cds_end": null,
"cds_length": 2586,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001329238.2"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK9",
"gene_hgnc_id": 18591,
"hgvs_c": "c.1135C>T",
"hgvs_p": "p.Arg379*",
"transcript": "ENST00000678531.1",
"protein_id": "ENSP00000503827.1",
"transcript_support_level": null,
"aa_start": 379,
"aa_end": null,
"aa_length": 861,
"cds_start": 1135,
"cds_end": null,
"cds_length": 2586,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000678531.1"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK9",
"gene_hgnc_id": 18591,
"hgvs_c": "c.1135C>T",
"hgvs_p": "p.Arg379*",
"transcript": "ENST00000678749.1",
"protein_id": "ENSP00000504104.1",
"transcript_support_level": null,
"aa_start": 379,
"aa_end": null,
"aa_length": 861,
"cds_start": 1135,
"cds_end": null,
"cds_length": 2586,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000678749.1"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK9",
"gene_hgnc_id": 18591,
"hgvs_c": "c.1489C>T",
"hgvs_p": "p.Arg497*",
"transcript": "ENST00000553823.6",
"protein_id": "ENSP00000452537.2",
"transcript_support_level": 5,
"aa_start": 497,
"aa_end": null,
"aa_length": 592,
"cds_start": 1489,
"cds_end": null,
"cds_length": 1779,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000553823.6"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK9",
"gene_hgnc_id": 18591,
"hgvs_c": "c.1135C>T",
"hgvs_p": "p.Arg379*",
"transcript": "XM_005268209.4",
"protein_id": "XP_005268266.1",
"transcript_support_level": null,
"aa_start": 379,
"aa_end": null,
"aa_length": 873,
"cds_start": 1135,
"cds_end": null,
"cds_length": 2622,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005268209.4"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK9",
"gene_hgnc_id": 18591,
"hgvs_c": "c.1135C>T",
"hgvs_p": "p.Arg379*",
"transcript": "XM_047431919.1",
"protein_id": "XP_047287875.1",
"transcript_support_level": null,
"aa_start": 379,
"aa_end": null,
"aa_length": 861,
"cds_start": 1135,
"cds_end": null,
"cds_length": 2586,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047431919.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK9",
"gene_hgnc_id": 18591,
"hgvs_c": "n.1613C>T",
"hgvs_p": null,
"transcript": "ENST00000556170.5",
"protein_id": null,
"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": "retained_intron",
"feature": "ENST00000556170.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK9",
"gene_hgnc_id": 18591,
"hgvs_c": "n.778C>T",
"hgvs_p": null,
"transcript": "ENST00000557026.5",
"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": "retained_intron",
"feature": "ENST00000557026.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK9",
"gene_hgnc_id": 18591,
"hgvs_c": "n.*925C>T",
"hgvs_p": null,
"transcript": "ENST00000557673.6",
"protein_id": "ENSP00000450943.2",
"transcript_support_level": 3,
"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": "ENST00000557673.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK9",
"gene_hgnc_id": 18591,
"hgvs_c": "n.*533C>T",
"hgvs_p": null,
"transcript": "ENST00000677700.1",
"protein_id": "ENSP00000503940.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000677700.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK9",
"gene_hgnc_id": 18591,
"hgvs_c": "n.*925C>T",
"hgvs_p": null,
"transcript": "ENST00000557673.6",
"protein_id": "ENSP00000450943.2",
"transcript_support_level": 3,
"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": "ENST00000557673.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEK9",
"gene_hgnc_id": 18591,
"hgvs_c": "n.*533C>T",
"hgvs_p": null,
"transcript": "ENST00000677700.1",
"protein_id": "ENSP00000503940.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000677700.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ZC2HC1C",
"gene_hgnc_id": 20354,
"hgvs_c": "n.*80-2346G>A",
"hgvs_p": null,
"transcript": "ENST00000673981.1",
"protein_id": "ENSP00000501014.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000673981.1"
}
],
"gene_symbol": "NEK9",
"gene_hgnc_id": 18591,
"dbsnp": "rs757011098",
"frequency_reference_population": 0.00000743593,
"hom_count_reference_population": 0,
"allele_count_reference_population": 12,
"gnomad_exomes_af": 0.00000752463,
"gnomad_genomes_af": 0.00000658241,
"gnomad_exomes_ac": 11,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6299999952316284,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.1599999964237213,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.63,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.237,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.16,
"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": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Moderate",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PVS1",
"PM2",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "NM_001329237.2",
"gene_symbol": "NEK9",
"hgnc_id": 18591,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1489C>T",
"hgvs_p": "p.Arg497*"
},
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000673981.1",
"gene_symbol": "ZC2HC1C",
"hgnc_id": 20354,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.*80-2346G>A",
"hgvs_p": null
}
],
"clinvar_disease": "NEK9-related lethal skeletal dysplasia",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "NEK9-related lethal skeletal dysplasia",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}