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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: 5-35654609-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=35654609&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 35654609,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000356031.8",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPEF2",
"gene_hgnc_id": 26293,
"hgvs_c": "c.861C>T",
"hgvs_p": "p.Asp287Asp",
"transcript": "NM_024867.4",
"protein_id": "NP_079143.3",
"transcript_support_level": null,
"aa_start": 287,
"aa_end": null,
"aa_length": 1822,
"cds_start": 861,
"cds_end": null,
"cds_length": 5469,
"cdna_start": 996,
"cdna_end": null,
"cdna_length": 5662,
"mane_select": "ENST00000356031.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPEF2",
"gene_hgnc_id": 26293,
"hgvs_c": "c.861C>T",
"hgvs_p": "p.Asp287Asp",
"transcript": "ENST00000356031.8",
"protein_id": "ENSP00000348314.3",
"transcript_support_level": 1,
"aa_start": 287,
"aa_end": null,
"aa_length": 1822,
"cds_start": 861,
"cds_end": null,
"cds_length": 5469,
"cdna_start": 996,
"cdna_end": null,
"cdna_length": 5662,
"mane_select": "NM_024867.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPEF2",
"gene_hgnc_id": 26293,
"hgvs_c": "c.861C>T",
"hgvs_p": "p.Asp287Asp",
"transcript": "ENST00000509059.5",
"protein_id": "ENSP00000421593.1",
"transcript_support_level": 1,
"aa_start": 287,
"aa_end": null,
"aa_length": 943,
"cds_start": 861,
"cds_end": null,
"cds_length": 2832,
"cdna_start": 1015,
"cdna_end": null,
"cdna_length": 4707,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPEF2",
"gene_hgnc_id": 26293,
"hgvs_c": "c.861C>T",
"hgvs_p": "p.Asp287Asp",
"transcript": "ENST00000282469.10",
"protein_id": "ENSP00000282469.6",
"transcript_support_level": 1,
"aa_start": 287,
"aa_end": null,
"aa_length": 514,
"cds_start": 861,
"cds_end": null,
"cds_length": 1545,
"cdna_start": 1015,
"cdna_end": null,
"cdna_length": 3026,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPEF2",
"gene_hgnc_id": 26293,
"hgvs_c": "c.861C>T",
"hgvs_p": "p.Asp287Asp",
"transcript": "ENST00000637569.1",
"protein_id": "ENSP00000490886.1",
"transcript_support_level": 5,
"aa_start": 287,
"aa_end": null,
"aa_length": 2169,
"cds_start": 861,
"cds_end": null,
"cds_length": 6510,
"cdna_start": 1015,
"cdna_end": null,
"cdna_length": 7350,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPEF2",
"gene_hgnc_id": 26293,
"hgvs_c": "c.861C>T",
"hgvs_p": "p.Asp287Asp",
"transcript": "ENST00000440995.6",
"protein_id": "ENSP00000412125.2",
"transcript_support_level": 5,
"aa_start": 287,
"aa_end": null,
"aa_length": 1818,
"cds_start": 861,
"cds_end": null,
"cds_length": 5457,
"cdna_start": 861,
"cdna_end": null,
"cdna_length": 5964,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPEF2",
"gene_hgnc_id": 26293,
"hgvs_c": "c.861C>T",
"hgvs_p": "p.Asp287Asp",
"transcript": "NM_144722.4",
"protein_id": "NP_653323.1",
"transcript_support_level": null,
"aa_start": 287,
"aa_end": null,
"aa_length": 514,
"cds_start": 861,
"cds_end": null,
"cds_length": 1545,
"cdna_start": 996,
"cdna_end": null,
"cdna_length": 3008,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPEF2",
"gene_hgnc_id": 26293,
"hgvs_c": "c.690C>T",
"hgvs_p": "p.Asp230Asp",
"transcript": "ENST00000510777.5",
"protein_id": "ENSP00000426259.1",
"transcript_support_level": 3,
"aa_start": 230,
"aa_end": null,
"aa_length": 239,
"cds_start": 690,
"cds_end": null,
"cds_length": 722,
"cdna_start": 768,
"cdna_end": null,
"cdna_length": 800,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 42,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPEF2",
"gene_hgnc_id": 26293,
"hgvs_c": "c.861C>T",
"hgvs_p": "p.Asp287Asp",
"transcript": "XM_011514135.4",
"protein_id": "XP_011512437.1",
"transcript_support_level": null,
"aa_start": 287,
"aa_end": null,
"aa_length": 2097,
"cds_start": 861,
"cds_end": null,
"cds_length": 6294,
"cdna_start": 996,
"cdna_end": null,
"cdna_length": 6740,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 42,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPEF2",
"gene_hgnc_id": 26293,
"hgvs_c": "c.861C>T",
"hgvs_p": "p.Asp287Asp",
"transcript": "XM_011514136.4",
"protein_id": "XP_011512438.1",
"transcript_support_level": null,
"aa_start": 287,
"aa_end": null,
"aa_length": 2096,
"cds_start": 861,
"cds_end": null,
"cds_length": 6291,
"cdna_start": 996,
"cdna_end": null,
"cdna_length": 6484,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 42,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPEF2",
"gene_hgnc_id": 26293,
"hgvs_c": "c.861C>T",
"hgvs_p": "p.Asp287Asp",
"transcript": "XM_011514137.4",
"protein_id": "XP_011512439.1",
"transcript_support_level": null,
"aa_start": 287,
"aa_end": null,
"aa_length": 2092,
"cds_start": 861,
"cds_end": null,
"cds_length": 6279,
"cdna_start": 996,
"cdna_end": null,
"cdna_length": 6725,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 42,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPEF2",
"gene_hgnc_id": 26293,
"hgvs_c": "c.861C>T",
"hgvs_p": "p.Asp287Asp",
"transcript": "XM_011514138.4",
"protein_id": "XP_011512440.1",
"transcript_support_level": null,
"aa_start": 287,
"aa_end": null,
"aa_length": 2089,
"cds_start": 861,
"cds_end": null,
"cds_length": 6270,
"cdna_start": 996,
"cdna_end": null,
"cdna_length": 6716,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPEF2",
"gene_hgnc_id": 26293,
"hgvs_c": "c.861C>T",
"hgvs_p": "p.Asp287Asp",
"transcript": "XM_011514139.4",
"protein_id": "XP_011512441.1",
"transcript_support_level": null,
"aa_start": 287,
"aa_end": null,
"aa_length": 2072,
"cds_start": 861,
"cds_end": null,
"cds_length": 6219,
"cdna_start": 996,
"cdna_end": null,
"cdna_length": 6665,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPEF2",
"gene_hgnc_id": 26293,
"hgvs_c": "c.690C>T",
"hgvs_p": "p.Asp230Asp",
"transcript": "XM_011514140.3",
"protein_id": "XP_011512442.1",
"transcript_support_level": null,
"aa_start": 230,
"aa_end": null,
"aa_length": 2040,
"cds_start": 690,
"cds_end": null,
"cds_length": 6123,
"cdna_start": 825,
"cdna_end": null,
"cdna_length": 6569,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPEF2",
"gene_hgnc_id": 26293,
"hgvs_c": "c.690C>T",
"hgvs_p": "p.Asp230Asp",
"transcript": "XM_017009880.3",
"protein_id": "XP_016865369.1",
"transcript_support_level": null,
"aa_start": 230,
"aa_end": null,
"aa_length": 2035,
"cds_start": 690,
"cds_end": null,
"cds_length": 6108,
"cdna_start": 825,
"cdna_end": null,
"cdna_length": 6554,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPEF2",
"gene_hgnc_id": 26293,
"hgvs_c": "c.435C>T",
"hgvs_p": "p.Asp145Asp",
"transcript": "XM_047417765.1",
"protein_id": "XP_047273721.1",
"transcript_support_level": null,
"aa_start": 145,
"aa_end": null,
"aa_length": 1955,
"cds_start": 435,
"cds_end": null,
"cds_length": 5868,
"cdna_start": 1387,
"cdna_end": null,
"cdna_length": 7131,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPEF2",
"gene_hgnc_id": 26293,
"hgvs_c": "c.435C>T",
"hgvs_p": "p.Asp145Asp",
"transcript": "XM_047417766.1",
"protein_id": "XP_047273722.1",
"transcript_support_level": null,
"aa_start": 145,
"aa_end": null,
"aa_length": 1955,
"cds_start": 435,
"cds_end": null,
"cds_length": 5868,
"cdna_start": 2457,
"cdna_end": null,
"cdna_length": 8201,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPEF2",
"gene_hgnc_id": 26293,
"hgvs_c": "c.861C>T",
"hgvs_p": "p.Asp287Asp",
"transcript": "XM_005248376.5",
"protein_id": "XP_005248433.1",
"transcript_support_level": null,
"aa_start": 287,
"aa_end": null,
"aa_length": 1823,
"cds_start": 861,
"cds_end": null,
"cds_length": 5472,
"cdna_start": 996,
"cdna_end": null,
"cdna_length": 5918,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPEF2",
"gene_hgnc_id": 26293,
"hgvs_c": "c.861C>T",
"hgvs_p": "p.Asp287Asp",
"transcript": "XM_005248377.5",
"protein_id": "XP_005248434.1",
"transcript_support_level": null,
"aa_start": 287,
"aa_end": null,
"aa_length": 1818,
"cds_start": 861,
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"cdna_start": 996,
"cdna_end": null,
"cdna_length": 5903,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPEF2",
"gene_hgnc_id": 26293,
"hgvs_c": "c.861C>T",
"hgvs_p": "p.Asp287Asp",
"transcript": "XM_047417767.1",
"protein_id": "XP_047273723.1",
"transcript_support_level": null,
"aa_start": 287,
"aa_end": null,
"aa_length": 1797,
"cds_start": 861,
"cds_end": null,
"cds_length": 5394,
"cdna_start": 996,
"cdna_end": null,
"cdna_length": 5587,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPEF2",
"gene_hgnc_id": 26293,
"hgvs_c": "c.690C>T",
"hgvs_p": "p.Asp230Asp",
"transcript": "XM_024446219.2",
"protein_id": "XP_024301987.1",
"transcript_support_level": null,
"aa_start": 230,
"aa_end": null,
"aa_length": 1740,
"cds_start": 690,
"cds_end": null,
"cds_length": 5223,
"cdna_start": 825,
"cdna_end": null,
"cdna_length": 5416,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPEF2",
"gene_hgnc_id": 26293,
"hgvs_c": "c.861C>T",
"hgvs_p": "p.Asp287Asp",
"transcript": "XM_047417768.1",
"protein_id": "XP_047273724.1",
"transcript_support_level": null,
"aa_start": 287,
"aa_end": null,
"aa_length": 1537,
"cds_start": 861,
"cds_end": null,
"cds_length": 4614,
"cdna_start": 996,
"cdna_end": null,
"cdna_length": 4835,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPEF2",
"gene_hgnc_id": 26293,
"hgvs_c": "c.861C>T",
"hgvs_p": "p.Asp287Asp",
"transcript": "XM_047417769.1",
"protein_id": "XP_047273725.1",
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}
],
"gene_symbol": "SPEF2",
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"dbsnp": "rs2270558",
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"computational_score_selected": -0.550000011920929,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
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"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.55,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.121,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
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"dbscsnv_ada_prediction": null,
"apogee2_score": null,
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"acmg_score": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000356031.8",
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"effects": [
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],
"inheritance_mode": "AR,AD",
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],
"clinvar_disease": "Spermatogenic failure 43,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:4",
"phenotype_combined": "not specified|not provided|Spermatogenic failure 43",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}