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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: 6-55439472-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=55439472&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 55439472,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_019036.3",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGCLL1",
"gene_hgnc_id": 21359,
"hgvs_c": "c.883G>A",
"hgvs_p": "p.Asp295Asn",
"transcript": "NM_001042406.2",
"protein_id": "NP_001035865.1",
"transcript_support_level": null,
"aa_start": 295,
"aa_end": null,
"aa_length": 340,
"cds_start": 883,
"cds_end": null,
"cds_length": 1023,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000274901.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001042406.2"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGCLL1",
"gene_hgnc_id": 21359,
"hgvs_c": "c.883G>A",
"hgvs_p": "p.Asp295Asn",
"transcript": "ENST00000274901.9",
"protein_id": "ENSP00000274901.4",
"transcript_support_level": 1,
"aa_start": 295,
"aa_end": null,
"aa_length": 340,
"cds_start": 883,
"cds_end": null,
"cds_length": 1023,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001042406.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000274901.9"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGCLL1",
"gene_hgnc_id": 21359,
"hgvs_c": "c.973G>A",
"hgvs_p": "p.Asp325Asn",
"transcript": "NM_019036.3",
"protein_id": "NP_061909.2",
"transcript_support_level": null,
"aa_start": 325,
"aa_end": null,
"aa_length": 370,
"cds_start": 973,
"cds_end": null,
"cds_length": 1113,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_019036.3"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGCLL1",
"gene_hgnc_id": 21359,
"hgvs_c": "c.973G>A",
"hgvs_p": "p.Asp325Asn",
"transcript": "ENST00000398661.6",
"protein_id": "ENSP00000381654.2",
"transcript_support_level": 2,
"aa_start": 325,
"aa_end": null,
"aa_length": 370,
"cds_start": 973,
"cds_end": null,
"cds_length": 1113,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000398661.6"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGCLL1",
"gene_hgnc_id": 21359,
"hgvs_c": "c.904G>A",
"hgvs_p": "p.Asp302Asn",
"transcript": "ENST00000957849.1",
"protein_id": "ENSP00000627908.1",
"transcript_support_level": null,
"aa_start": 302,
"aa_end": null,
"aa_length": 347,
"cds_start": 904,
"cds_end": null,
"cds_length": 1044,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000957849.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGCLL1",
"gene_hgnc_id": 21359,
"hgvs_c": "c.808G>A",
"hgvs_p": "p.Asp270Asn",
"transcript": "ENST00000957848.1",
"protein_id": "ENSP00000627907.1",
"transcript_support_level": null,
"aa_start": 270,
"aa_end": null,
"aa_length": 315,
"cds_start": 808,
"cds_end": null,
"cds_length": 948,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000957848.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGCLL1",
"gene_hgnc_id": 21359,
"hgvs_c": "c.787G>A",
"hgvs_p": "p.Asp263Asn",
"transcript": "NM_001287741.2",
"protein_id": "NP_001274670.1",
"transcript_support_level": null,
"aa_start": 263,
"aa_end": null,
"aa_length": 308,
"cds_start": 787,
"cds_end": null,
"cds_length": 927,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001287741.2"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGCLL1",
"gene_hgnc_id": 21359,
"hgvs_c": "c.787G>A",
"hgvs_p": "p.Asp263Asn",
"transcript": "ENST00000308161.8",
"protein_id": "ENSP00000309737.4",
"transcript_support_level": 2,
"aa_start": 263,
"aa_end": null,
"aa_length": 308,
"cds_start": 787,
"cds_end": null,
"cds_length": 927,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000308161.8"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGCLL1",
"gene_hgnc_id": 21359,
"hgvs_c": "c.586G>A",
"hgvs_p": "p.Asp196Asn",
"transcript": "NM_001287746.2",
"protein_id": "NP_001274675.1",
"transcript_support_level": null,
"aa_start": 196,
"aa_end": null,
"aa_length": 241,
"cds_start": 586,
"cds_end": null,
"cds_length": 726,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001287746.2"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGCLL1",
"gene_hgnc_id": 21359,
"hgvs_c": "c.574G>A",
"hgvs_p": "p.Asp192Asn",
"transcript": "NM_001287753.2",
"protein_id": "NP_001274682.1",
"transcript_support_level": null,
"aa_start": 192,
"aa_end": null,
"aa_length": 237,
"cds_start": 574,
"cds_end": null,
"cds_length": 714,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001287753.2"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGCLL1",
"gene_hgnc_id": 21359,
"hgvs_c": "c.574G>A",
"hgvs_p": "p.Asp192Asn",
"transcript": "ENST00000370850.6",
"protein_id": "ENSP00000359887.2",
"transcript_support_level": 2,
"aa_start": 192,
"aa_end": null,
"aa_length": 237,
"cds_start": 574,
"cds_end": null,
"cds_length": 714,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000370850.6"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGCLL1",
"gene_hgnc_id": 21359,
"hgvs_c": "c.385G>A",
"hgvs_p": "p.Asp129Asn",
"transcript": "ENST00000508459.5",
"protein_id": "ENSP00000424309.1",
"transcript_support_level": 2,
"aa_start": 129,
"aa_end": null,
"aa_length": 174,
"cds_start": 385,
"cds_end": null,
"cds_length": 525,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000508459.5"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGCLL1",
"gene_hgnc_id": 21359,
"hgvs_c": "c.196G>A",
"hgvs_p": "p.Asp66Asn",
"transcript": "ENST00000893699.1",
"protein_id": "ENSP00000563758.1",
"transcript_support_level": null,
"aa_start": 66,
"aa_end": null,
"aa_length": 111,
"cds_start": 196,
"cds_end": null,
"cds_length": 336,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000893699.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGCLL1",
"gene_hgnc_id": 21359,
"hgvs_c": "c.787G>A",
"hgvs_p": "p.Asp263Asn",
"transcript": "XM_047418902.1",
"protein_id": "XP_047274858.1",
"transcript_support_level": null,
"aa_start": 263,
"aa_end": null,
"aa_length": 308,
"cds_start": 787,
"cds_end": null,
"cds_length": 927,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047418902.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGCLL1",
"gene_hgnc_id": 21359,
"hgvs_c": "c.586G>A",
"hgvs_p": "p.Asp196Asn",
"transcript": "XM_047418903.1",
"protein_id": "XP_047274859.1",
"transcript_support_level": null,
"aa_start": 196,
"aa_end": null,
"aa_length": 241,
"cds_start": 586,
"cds_end": null,
"cds_length": 726,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047418903.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGCLL1",
"gene_hgnc_id": 21359,
"hgvs_c": "c.586G>A",
"hgvs_p": "p.Asp196Asn",
"transcript": "XM_047418904.1",
"protein_id": "XP_047274860.1",
"transcript_support_level": null,
"aa_start": 196,
"aa_end": null,
"aa_length": 241,
"cds_start": 586,
"cds_end": null,
"cds_length": 726,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047418904.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGCLL1",
"gene_hgnc_id": 21359,
"hgvs_c": "n.*817G>A",
"hgvs_p": null,
"transcript": "ENST00000370852.6",
"protein_id": "ENSP00000359889.2",
"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": "nonsense_mediated_decay",
"feature": "ENST00000370852.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGCLL1",
"gene_hgnc_id": 21359,
"hgvs_c": "n.129G>A",
"hgvs_p": null,
"transcript": "ENST00000507223.1",
"protein_id": null,
"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": "pseudogene",
"feature": "ENST00000507223.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGCLL1",
"gene_hgnc_id": 21359,
"hgvs_c": "n.*888G>A",
"hgvs_p": null,
"transcript": "ENST00000515546.2",
"protein_id": "ENSP00000426054.1",
"transcript_support_level": 4,
"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": "ENST00000515546.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGCLL1",
"gene_hgnc_id": 21359,
"hgvs_c": "n.522G>A",
"hgvs_p": null,
"transcript": "NR_109869.2",
"protein_id": null,
"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": "pseudogene",
"feature": "NR_109869.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGCLL1",
"gene_hgnc_id": 21359,
"hgvs_c": "n.*817G>A",
"hgvs_p": null,
"transcript": "ENST00000370852.6",
"protein_id": "ENSP00000359889.2",
"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": "nonsense_mediated_decay",
"feature": "ENST00000370852.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HMGCLL1",
"gene_hgnc_id": 21359,
"hgvs_c": "n.*888G>A",
"hgvs_p": null,
"transcript": "ENST00000515546.2",
"protein_id": "ENSP00000426054.1",
"transcript_support_level": 4,
"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": "ENST00000515546.2"
}
],
"gene_symbol": "HMGCLL1",
"gene_hgnc_id": 21359,
"dbsnp": "rs764166829",
"frequency_reference_population": 0.000012402085,
"hom_count_reference_population": 1,
"allele_count_reference_population": 20,
"gnomad_exomes_af": 0.0000123239,
"gnomad_genomes_af": 0.0000131527,
"gnomad_exomes_ac": 18,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9193527698516846,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.18000000715255737,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.892,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9107,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.08,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.892,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.18,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3_Moderate",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_019036.3",
"gene_symbol": "HMGCLL1",
"hgnc_id": 21359,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.973G>A",
"hgvs_p": "p.Asp325Asn"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}