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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: 14-88416725-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=88416725&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "14",
"pos": 88416725,
"ref": "C",
"alt": "T",
"effect": "stop_gained",
"transcript": "NM_018418.5",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA7",
"gene_hgnc_id": 20423,
"hgvs_c": "c.253C>T",
"hgvs_p": "p.Arg85*",
"transcript": "NM_018418.5",
"protein_id": "NP_060888.2",
"transcript_support_level": null,
"aa_start": 85,
"aa_end": null,
"aa_length": 599,
"cds_start": 253,
"cds_end": null,
"cds_length": 1800,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000393545.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_018418.5"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA7",
"gene_hgnc_id": 20423,
"hgvs_c": "c.253C>T",
"hgvs_p": "p.Arg85*",
"transcript": "ENST00000393545.9",
"protein_id": "ENSP00000377176.4",
"transcript_support_level": 1,
"aa_start": 85,
"aa_end": null,
"aa_length": 599,
"cds_start": 253,
"cds_end": null,
"cds_length": 1800,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_018418.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000393545.9"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA7",
"gene_hgnc_id": 20423,
"hgvs_c": "c.157C>T",
"hgvs_p": "p.Arg53*",
"transcript": "ENST00000356583.9",
"protein_id": "ENSP00000348991.5",
"transcript_support_level": 1,
"aa_start": 53,
"aa_end": null,
"aa_length": 567,
"cds_start": 157,
"cds_end": null,
"cds_length": 1704,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000356583.9"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA7",
"gene_hgnc_id": 20423,
"hgvs_c": "c.157C>T",
"hgvs_p": "p.Arg53*",
"transcript": "ENST00000556553.5",
"protein_id": "ENSP00000451128.1",
"transcript_support_level": 1,
"aa_start": 53,
"aa_end": null,
"aa_length": 567,
"cds_start": 157,
"cds_end": null,
"cds_length": 1704,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000556553.5"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA7",
"gene_hgnc_id": 20423,
"hgvs_c": "c.253C>T",
"hgvs_p": "p.Arg85*",
"transcript": "ENST00000879181.1",
"protein_id": "ENSP00000549240.1",
"transcript_support_level": null,
"aa_start": 85,
"aa_end": null,
"aa_length": 581,
"cds_start": 253,
"cds_end": null,
"cds_length": 1746,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000879181.1"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA7",
"gene_hgnc_id": 20423,
"hgvs_c": "c.157C>T",
"hgvs_p": "p.Arg53*",
"transcript": "NM_001040428.4",
"protein_id": "NP_001035518.1",
"transcript_support_level": null,
"aa_start": 53,
"aa_end": null,
"aa_length": 567,
"cds_start": 157,
"cds_end": null,
"cds_length": 1704,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001040428.4"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA7",
"gene_hgnc_id": 20423,
"hgvs_c": "c.253C>T",
"hgvs_p": "p.Arg85*",
"transcript": "ENST00000045347.11",
"protein_id": "ENSP00000045347.7",
"transcript_support_level": 5,
"aa_start": 85,
"aa_end": null,
"aa_length": 458,
"cds_start": 253,
"cds_end": null,
"cds_length": 1377,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000045347.11"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA7",
"gene_hgnc_id": 20423,
"hgvs_c": "c.211C>T",
"hgvs_p": "p.Arg71*",
"transcript": "ENST00000553885.5",
"protein_id": "ENSP00000450606.1",
"transcript_support_level": 3,
"aa_start": 71,
"aa_end": null,
"aa_length": 227,
"cds_start": 211,
"cds_end": null,
"cds_length": 684,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000553885.5"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA7",
"gene_hgnc_id": 20423,
"hgvs_c": "c.82C>T",
"hgvs_p": "p.Arg28*",
"transcript": "ENST00000555401.5",
"protein_id": "ENSP00000452435.1",
"transcript_support_level": 3,
"aa_start": 28,
"aa_end": null,
"aa_length": 137,
"cds_start": 82,
"cds_end": null,
"cds_length": 416,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000555401.5"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA7",
"gene_hgnc_id": 20423,
"hgvs_c": "c.253C>T",
"hgvs_p": "p.Arg85*",
"transcript": "XM_005267851.2",
"protein_id": "XP_005267908.1",
"transcript_support_level": null,
"aa_start": 85,
"aa_end": null,
"aa_length": 600,
"cds_start": 253,
"cds_end": null,
"cds_length": 1803,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005267851.2"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA7",
"gene_hgnc_id": 20423,
"hgvs_c": "c.157C>T",
"hgvs_p": "p.Arg53*",
"transcript": "XM_005267852.3",
"protein_id": "XP_005267909.1",
"transcript_support_level": null,
"aa_start": 53,
"aa_end": null,
"aa_length": 568,
"cds_start": 157,
"cds_end": null,
"cds_length": 1707,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005267852.3"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA7",
"gene_hgnc_id": 20423,
"hgvs_c": "c.82C>T",
"hgvs_p": "p.Arg28*",
"transcript": "XM_011536952.2",
"protein_id": "XP_011535254.1",
"transcript_support_level": null,
"aa_start": 28,
"aa_end": null,
"aa_length": 543,
"cds_start": 82,
"cds_end": null,
"cds_length": 1632,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011536952.2"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA7",
"gene_hgnc_id": 20423,
"hgvs_c": "c.82C>T",
"hgvs_p": "p.Arg28*",
"transcript": "XM_024449660.2",
"protein_id": "XP_024305428.1",
"transcript_support_level": null,
"aa_start": 28,
"aa_end": null,
"aa_length": 542,
"cds_start": 82,
"cds_end": null,
"cds_length": 1629,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024449660.2"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA7",
"gene_hgnc_id": 20423,
"hgvs_c": "c.253C>T",
"hgvs_p": "p.Arg85*",
"transcript": "XM_006720204.2",
"protein_id": "XP_006720267.1",
"transcript_support_level": null,
"aa_start": 85,
"aa_end": null,
"aa_length": 445,
"cds_start": 253,
"cds_end": null,
"cds_length": 1338,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006720204.2"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA7",
"gene_hgnc_id": 20423,
"hgvs_c": "c.253C>T",
"hgvs_p": "p.Arg85*",
"transcript": "XM_006720205.2",
"protein_id": "XP_006720268.1",
"transcript_support_level": null,
"aa_start": 85,
"aa_end": null,
"aa_length": 434,
"cds_start": 253,
"cds_end": null,
"cds_length": 1305,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006720205.2"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA7",
"gene_hgnc_id": 20423,
"hgvs_c": "c.253C>T",
"hgvs_p": "p.Arg85*",
"transcript": "XM_047431581.1",
"protein_id": "XP_047287537.1",
"transcript_support_level": null,
"aa_start": 85,
"aa_end": null,
"aa_length": 433,
"cds_start": 253,
"cds_end": null,
"cds_length": 1302,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047431581.1"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA7",
"gene_hgnc_id": 20423,
"hgvs_c": "c.157C>T",
"hgvs_p": "p.Arg53*",
"transcript": "XM_047431582.1",
"protein_id": "XP_047287538.1",
"transcript_support_level": null,
"aa_start": 53,
"aa_end": null,
"aa_length": 412,
"cds_start": 157,
"cds_end": null,
"cds_length": 1239,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047431582.1"
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA7",
"gene_hgnc_id": 20423,
"hgvs_c": "c.157C>T",
"hgvs_p": "p.Arg53*",
"transcript": "XM_047431584.1",
"protein_id": "XP_047287540.1",
"transcript_support_level": null,
"aa_start": 53,
"aa_end": null,
"aa_length": 401,
"cds_start": 157,
"cds_end": null,
"cds_length": 1206,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047431584.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA7",
"gene_hgnc_id": 20423,
"hgvs_c": "n.381C>T",
"hgvs_p": null,
"transcript": "ENST00000553626.5",
"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": "ENST00000553626.5"
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA7",
"gene_hgnc_id": 20423,
"hgvs_c": "n.*128C>T",
"hgvs_p": null,
"transcript": "ENST00000553908.5",
"protein_id": "ENSP00000452546.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000553908.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA7",
"gene_hgnc_id": 20423,
"hgvs_c": "n.*210C>T",
"hgvs_p": null,
"transcript": "ENST00000554168.5",
"protein_id": "ENSP00000451663.1",
"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": "ENST00000554168.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPATA7",
"gene_hgnc_id": 20423,
"hgvs_c": "n.*269C>T",
"hgvs_p": null,
"transcript": "ENST00000555356.5",
"protein_id": "ENSP00000450654.1",
"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": "ENST00000555356.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
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],
"gene_symbol": "SPATA7",
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"dbsnp": "rs140287375",
"frequency_reference_population": 0.0000440226,
"hom_count_reference_population": 0,
"allele_count_reference_population": 71,
"gnomad_exomes_af": 0.0000438071,
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"gnomad_exomes_ac": 64,
"gnomad_genomes_ac": 7,
"gnomad_exomes_homalt": 0,
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"gnomad_mito_homoplasmic": null,
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"computational_score_selected": 0.5600000023841858,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.56,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 1.563,
"phylop100way_prediction": "Benign",
"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": 16,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 16,
"benign_score": 0,
"pathogenic_score": 16,
"criteria": [
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"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_018418.5",
"gene_symbol": "SPATA7",
"hgnc_id": 20423,
"effects": [
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],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.253C>T",
"hgvs_p": "p.Arg85*"
}
],
"clinvar_disease": " variable age at onset,Leber congenital amaurosis 3,Retinal dystrophy,Retinitis pigmentosa 94,SPATA7-related disorder,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:6 LP:1",
"phenotype_combined": "Leber congenital amaurosis 3|SPATA7-related disorder|Retinal dystrophy|Retinitis pigmentosa 94, variable age at onset|not provided",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}