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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: X-41346399-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=41346399&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 41346399,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001356.5",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX3X",
"gene_hgnc_id": 2745,
"hgvs_c": "c.1486G>A",
"hgvs_p": "p.Val496Met",
"transcript": "NM_001356.5",
"protein_id": "NP_001347.3",
"transcript_support_level": null,
"aa_start": 496,
"aa_end": null,
"aa_length": 662,
"cds_start": 1486,
"cds_end": null,
"cds_length": 1989,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000644876.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001356.5"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX3X",
"gene_hgnc_id": 2745,
"hgvs_c": "c.1486G>A",
"hgvs_p": "p.Val496Met",
"transcript": "ENST00000644876.2",
"protein_id": "ENSP00000494040.1",
"transcript_support_level": null,
"aa_start": 496,
"aa_end": null,
"aa_length": 662,
"cds_start": 1486,
"cds_end": null,
"cds_length": 1989,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001356.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000644876.2"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX3X",
"gene_hgnc_id": 2745,
"hgvs_c": "c.1483G>A",
"hgvs_p": "p.Val495Met",
"transcript": "ENST00000399959.7",
"protein_id": "ENSP00000382840.3",
"transcript_support_level": 1,
"aa_start": 495,
"aa_end": null,
"aa_length": 661,
"cds_start": 1483,
"cds_end": null,
"cds_length": 1986,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000399959.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX3X",
"gene_hgnc_id": 2745,
"hgvs_c": "n.1486G>A",
"hgvs_p": null,
"transcript": "ENST00000478993.5",
"protein_id": "ENSP00000478443.1",
"transcript_support_level": 1,
"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": "ENST00000478993.5"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX3X",
"gene_hgnc_id": 2745,
"hgvs_c": "c.1486G>A",
"hgvs_p": "p.Val496Met",
"transcript": "ENST00000625837.2",
"protein_id": "ENSP00000486306.1",
"transcript_support_level": 5,
"aa_start": 496,
"aa_end": null,
"aa_length": 733,
"cds_start": 1486,
"cds_end": null,
"cds_length": 2202,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000625837.2"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX3X",
"gene_hgnc_id": 2745,
"hgvs_c": "c.1651G>A",
"hgvs_p": "p.Val551Met",
"transcript": "ENST00000875789.1",
"protein_id": "ENSP00000545848.1",
"transcript_support_level": null,
"aa_start": 551,
"aa_end": null,
"aa_length": 717,
"cds_start": 1651,
"cds_end": null,
"cds_length": 2154,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875789.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX3X",
"gene_hgnc_id": 2745,
"hgvs_c": "c.1648G>A",
"hgvs_p": "p.Val550Met",
"transcript": "ENST00000644109.1",
"protein_id": "ENSP00000494952.1",
"transcript_support_level": null,
"aa_start": 550,
"aa_end": null,
"aa_length": 716,
"cds_start": 1648,
"cds_end": null,
"cds_length": 2151,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000644109.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX3X",
"gene_hgnc_id": 2745,
"hgvs_c": "c.1651G>A",
"hgvs_p": "p.Val551Met",
"transcript": "ENST00000875787.1",
"protein_id": "ENSP00000545846.1",
"transcript_support_level": null,
"aa_start": 551,
"aa_end": null,
"aa_length": 716,
"cds_start": 1651,
"cds_end": null,
"cds_length": 2151,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875787.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX3X",
"gene_hgnc_id": 2745,
"hgvs_c": "c.1486G>A",
"hgvs_p": "p.Val496Met",
"transcript": "ENST00000629496.3",
"protein_id": "ENSP00000487224.1",
"transcript_support_level": 5,
"aa_start": 496,
"aa_end": null,
"aa_length": 662,
"cds_start": 1486,
"cds_end": null,
"cds_length": 1989,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000629496.3"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX3X",
"gene_hgnc_id": 2745,
"hgvs_c": "c.1486G>A",
"hgvs_p": "p.Val496Met",
"transcript": "ENST00000644513.1",
"protein_id": "ENSP00000493819.1",
"transcript_support_level": null,
"aa_start": 496,
"aa_end": null,
"aa_length": 662,
"cds_start": 1486,
"cds_end": null,
"cds_length": 1989,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000644513.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX3X",
"gene_hgnc_id": 2745,
"hgvs_c": "c.1486G>A",
"hgvs_p": "p.Val496Met",
"transcript": "ENST00000875792.1",
"protein_id": "ENSP00000545851.1",
"transcript_support_level": null,
"aa_start": 496,
"aa_end": null,
"aa_length": 662,
"cds_start": 1486,
"cds_end": null,
"cds_length": 1989,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875792.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX3X",
"gene_hgnc_id": 2745,
"hgvs_c": "c.1486G>A",
"hgvs_p": "p.Val496Met",
"transcript": "NM_001193416.3",
"protein_id": "NP_001180345.1",
"transcript_support_level": null,
"aa_start": 496,
"aa_end": null,
"aa_length": 661,
"cds_start": 1486,
"cds_end": null,
"cds_length": 1986,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001193416.3"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX3X",
"gene_hgnc_id": 2745,
"hgvs_c": "c.1486G>A",
"hgvs_p": "p.Val496Met",
"transcript": "ENST00000646319.1",
"protein_id": "ENSP00000495377.1",
"transcript_support_level": null,
"aa_start": 496,
"aa_end": null,
"aa_length": 661,
"cds_start": 1486,
"cds_end": null,
"cds_length": 1986,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000646319.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX3X",
"gene_hgnc_id": 2745,
"hgvs_c": "c.1486G>A",
"hgvs_p": "p.Val496Met",
"transcript": "ENST00000875784.1",
"protein_id": "ENSP00000545843.1",
"transcript_support_level": null,
"aa_start": 496,
"aa_end": null,
"aa_length": 661,
"cds_start": 1486,
"cds_end": null,
"cds_length": 1986,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875784.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX3X",
"gene_hgnc_id": 2745,
"hgvs_c": "c.1483G>A",
"hgvs_p": "p.Val495Met",
"transcript": "ENST00000644074.1",
"protein_id": "ENSP00000496663.1",
"transcript_support_level": null,
"aa_start": 495,
"aa_end": null,
"aa_length": 660,
"cds_start": 1483,
"cds_end": null,
"cds_length": 1983,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000644074.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX3X",
"gene_hgnc_id": 2745,
"hgvs_c": "c.1486G>A",
"hgvs_p": "p.Val496Met",
"transcript": "ENST00000875783.1",
"protein_id": "ENSP00000545842.1",
"transcript_support_level": null,
"aa_start": 496,
"aa_end": null,
"aa_length": 660,
"cds_start": 1486,
"cds_end": null,
"cds_length": 1983,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875783.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX3X",
"gene_hgnc_id": 2745,
"hgvs_c": "c.1486G>A",
"hgvs_p": "p.Val496Met",
"transcript": "ENST00000875788.1",
"protein_id": "ENSP00000545847.1",
"transcript_support_level": null,
"aa_start": 496,
"aa_end": null,
"aa_length": 654,
"cds_start": 1486,
"cds_end": null,
"cds_length": 1965,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875788.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX3X",
"gene_hgnc_id": 2745,
"hgvs_c": "c.1486G>A",
"hgvs_p": "p.Val496Met",
"transcript": "ENST00000875786.1",
"protein_id": "ENSP00000545845.1",
"transcript_support_level": null,
"aa_start": 496,
"aa_end": null,
"aa_length": 653,
"cds_start": 1486,
"cds_end": null,
"cds_length": 1962,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875786.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX3X",
"gene_hgnc_id": 2745,
"hgvs_c": "c.1486G>A",
"hgvs_p": "p.Val496Met",
"transcript": "ENST00000875791.1",
"protein_id": "ENSP00000545850.1",
"transcript_support_level": null,
"aa_start": 496,
"aa_end": null,
"aa_length": 650,
"cds_start": 1486,
"cds_end": null,
"cds_length": 1953,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000875791.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX3X",
"gene_hgnc_id": 2745,
"hgvs_c": "c.1444G>A",
"hgvs_p": "p.Val482Met",
"transcript": "ENST00000644073.1",
"protein_id": "ENSP00000493475.1",
"transcript_support_level": null,
"aa_start": 482,
"aa_end": null,
"aa_length": 647,
"cds_start": 1444,
"cds_end": null,
"cds_length": 1944,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000644073.1"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX3X",
"gene_hgnc_id": 2745,
"hgvs_c": "c.1438G>A",
"hgvs_p": "p.Val480Met",
"transcript": "NM_001193417.3",
"protein_id": "NP_001180346.1",
"transcript_support_level": null,
"aa_start": 480,
"aa_end": null,
"aa_length": 646,
"cds_start": 1438,
"cds_end": null,
"cds_length": 1941,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001193417.3"
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX3X",
"gene_hgnc_id": 2745,
"hgvs_c": "c.1438G>A",
"hgvs_p": "p.Val480Met",
"transcript": "ENST00000457138.7",
"protein_id": "ENSP00000392494.2",
"transcript_support_level": 2,
"aa_start": 480,
"aa_end": null,
"aa_length": 646,
"cds_start": 1438,
"cds_end": null,
"cds_length": 1941,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
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{
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],
"gene_symbol": "DDX3X",
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"dbsnp": "rs1555954154",
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"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
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"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
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"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8296998739242554,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.551,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9947,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.21,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.941,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
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"apogee2_score": null,
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"mitotip_score": null,
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"acmg_score": 10,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP2,PP3,PP5_Moderate",
"acmg_by_gene": [
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP2",
"PP3",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "NM_001356.5",
"gene_symbol": "DDX3X",
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"effects": [
"missense_variant"
],
"inheritance_mode": "XL,AR",
"hgvs_c": "c.1486G>A",
"hgvs_p": "p.Val496Met"
}
],
"clinvar_disease": " X-linked 102,Intellectual disability",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1 O:1",
"phenotype_combined": "Intellectual disability, X-linked 102",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}