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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: 3-58653724-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=58653724&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 58653724,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_138805.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAM3D",
"gene_hgnc_id": 18665,
"hgvs_c": "c.71G>A",
"hgvs_p": "p.Arg24Gln",
"transcript": "NM_138805.3",
"protein_id": "NP_620160.1",
"transcript_support_level": null,
"aa_start": 24,
"aa_end": null,
"aa_length": 224,
"cds_start": 71,
"cds_end": null,
"cds_length": 675,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000358781.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_138805.3"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAM3D",
"gene_hgnc_id": 18665,
"hgvs_c": "c.71G>A",
"hgvs_p": "p.Arg24Gln",
"transcript": "ENST00000358781.7",
"protein_id": "ENSP00000351632.2",
"transcript_support_level": 1,
"aa_start": 24,
"aa_end": null,
"aa_length": 224,
"cds_start": 71,
"cds_end": null,
"cds_length": 675,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_138805.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000358781.7"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAM3D",
"gene_hgnc_id": 18665,
"hgvs_c": "c.74G>A",
"hgvs_p": "p.Arg25Gln",
"transcript": "ENST00000876442.1",
"protein_id": "ENSP00000546501.1",
"transcript_support_level": null,
"aa_start": 25,
"aa_end": null,
"aa_length": 239,
"cds_start": 74,
"cds_end": null,
"cds_length": 720,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000876442.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAM3D",
"gene_hgnc_id": 18665,
"hgvs_c": "c.89G>A",
"hgvs_p": "p.Arg30Gln",
"transcript": "ENST00000876443.1",
"protein_id": "ENSP00000546502.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 230,
"cds_start": 89,
"cds_end": null,
"cds_length": 693,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000876443.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAM3D",
"gene_hgnc_id": 18665,
"hgvs_c": "c.89G>A",
"hgvs_p": "p.Arg30Gln",
"transcript": "ENST00000876440.1",
"protein_id": "ENSP00000546499.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 229,
"cds_start": 89,
"cds_end": null,
"cds_length": 690,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000876440.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAM3D",
"gene_hgnc_id": 18665,
"hgvs_c": "c.74G>A",
"hgvs_p": "p.Arg25Gln",
"transcript": "ENST00000876438.1",
"protein_id": "ENSP00000546497.1",
"transcript_support_level": null,
"aa_start": 25,
"aa_end": null,
"aa_length": 225,
"cds_start": 74,
"cds_end": null,
"cds_length": 678,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000876438.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAM3D",
"gene_hgnc_id": 18665,
"hgvs_c": "c.74G>A",
"hgvs_p": "p.Arg25Gln",
"transcript": "ENST00000951614.1",
"protein_id": "ENSP00000621673.1",
"transcript_support_level": null,
"aa_start": 25,
"aa_end": null,
"aa_length": 225,
"cds_start": 74,
"cds_end": null,
"cds_length": 678,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951614.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAM3D",
"gene_hgnc_id": 18665,
"hgvs_c": "c.71G>A",
"hgvs_p": "p.Arg24Gln",
"transcript": "ENST00000876435.1",
"protein_id": "ENSP00000546494.1",
"transcript_support_level": null,
"aa_start": 24,
"aa_end": null,
"aa_length": 224,
"cds_start": 71,
"cds_end": null,
"cds_length": 675,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000876435.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAM3D",
"gene_hgnc_id": 18665,
"hgvs_c": "c.74G>A",
"hgvs_p": "p.Arg25Gln",
"transcript": "ENST00000876436.1",
"protein_id": "ENSP00000546495.1",
"transcript_support_level": null,
"aa_start": 25,
"aa_end": null,
"aa_length": 224,
"cds_start": 74,
"cds_end": null,
"cds_length": 675,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000876436.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAM3D",
"gene_hgnc_id": 18665,
"hgvs_c": "c.71G>A",
"hgvs_p": "p.Arg24Gln",
"transcript": "ENST00000876444.1",
"protein_id": "ENSP00000546503.1",
"transcript_support_level": null,
"aa_start": 24,
"aa_end": null,
"aa_length": 224,
"cds_start": 71,
"cds_end": null,
"cds_length": 675,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000876444.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAM3D",
"gene_hgnc_id": 18665,
"hgvs_c": "c.71G>A",
"hgvs_p": "p.Arg24Gln",
"transcript": "ENST00000876446.1",
"protein_id": "ENSP00000546505.1",
"transcript_support_level": null,
"aa_start": 24,
"aa_end": null,
"aa_length": 224,
"cds_start": 71,
"cds_end": null,
"cds_length": 675,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000876446.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAM3D",
"gene_hgnc_id": 18665,
"hgvs_c": "c.71G>A",
"hgvs_p": "p.Arg24Gln",
"transcript": "ENST00000951609.1",
"protein_id": "ENSP00000621668.1",
"transcript_support_level": null,
"aa_start": 24,
"aa_end": null,
"aa_length": 224,
"cds_start": 71,
"cds_end": null,
"cds_length": 675,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951609.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAM3D",
"gene_hgnc_id": 18665,
"hgvs_c": "c.71G>A",
"hgvs_p": "p.Arg24Gln",
"transcript": "ENST00000951611.1",
"protein_id": "ENSP00000621670.1",
"transcript_support_level": null,
"aa_start": 24,
"aa_end": null,
"aa_length": 224,
"cds_start": 71,
"cds_end": null,
"cds_length": 675,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951611.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAM3D",
"gene_hgnc_id": 18665,
"hgvs_c": "c.71G>A",
"hgvs_p": "p.Arg24Gln",
"transcript": "ENST00000951613.1",
"protein_id": "ENSP00000621672.1",
"transcript_support_level": null,
"aa_start": 24,
"aa_end": null,
"aa_length": 224,
"cds_start": 71,
"cds_end": null,
"cds_length": 675,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951613.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAM3D",
"gene_hgnc_id": 18665,
"hgvs_c": "c.71G>A",
"hgvs_p": "p.Arg24Gln",
"transcript": "ENST00000876434.1",
"protein_id": "ENSP00000546493.1",
"transcript_support_level": null,
"aa_start": 24,
"aa_end": null,
"aa_length": 223,
"cds_start": 71,
"cds_end": null,
"cds_length": 672,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000876434.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAM3D",
"gene_hgnc_id": 18665,
"hgvs_c": "c.71G>A",
"hgvs_p": "p.Arg24Gln",
"transcript": "ENST00000876437.1",
"protein_id": "ENSP00000546496.1",
"transcript_support_level": null,
"aa_start": 24,
"aa_end": null,
"aa_length": 223,
"cds_start": 71,
"cds_end": null,
"cds_length": 672,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000876437.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAM3D",
"gene_hgnc_id": 18665,
"hgvs_c": "c.71G>A",
"hgvs_p": "p.Arg24Gln",
"transcript": "ENST00000876445.1",
"protein_id": "ENSP00000546504.1",
"transcript_support_level": null,
"aa_start": 24,
"aa_end": null,
"aa_length": 223,
"cds_start": 71,
"cds_end": null,
"cds_length": 672,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000876445.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAM3D",
"gene_hgnc_id": 18665,
"hgvs_c": "c.71G>A",
"hgvs_p": "p.Arg24Gln",
"transcript": "ENST00000876447.1",
"protein_id": "ENSP00000546506.1",
"transcript_support_level": null,
"aa_start": 24,
"aa_end": null,
"aa_length": 223,
"cds_start": 71,
"cds_end": null,
"cds_length": 672,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000876447.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAM3D",
"gene_hgnc_id": 18665,
"hgvs_c": "c.35G>A",
"hgvs_p": "p.Arg12Gln",
"transcript": "ENST00000951608.1",
"protein_id": "ENSP00000621667.1",
"transcript_support_level": null,
"aa_start": 12,
"aa_end": null,
"aa_length": 212,
"cds_start": 35,
"cds_end": null,
"cds_length": 639,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951608.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAM3D",
"gene_hgnc_id": 18665,
"hgvs_c": "c.35G>A",
"hgvs_p": "p.Arg12Gln",
"transcript": "ENST00000876441.1",
"protein_id": "ENSP00000546500.1",
"transcript_support_level": null,
"aa_start": 12,
"aa_end": null,
"aa_length": 211,
"cds_start": 35,
"cds_end": null,
"cds_length": 636,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000876441.1"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAM3D",
"gene_hgnc_id": 18665,
"hgvs_c": "c.71G>A",
"hgvs_p": "p.Arg24Gln",
"transcript": "ENST00000483787.5",
"protein_id": "ENSP00000417099.1",
"transcript_support_level": 5,
"aa_start": 24,
"aa_end": null,
"aa_length": 150,
"cds_start": 71,
"cds_end": null,
"cds_length": 454,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000483787.5"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAM3D",
"gene_hgnc_id": 18665,
"hgvs_c": "c.71G>A",
"hgvs_p": "p.Arg24Gln",
"transcript": "ENST00000498347.1",
"protein_id": "ENSP00000418982.1",
"transcript_support_level": 2,
"aa_start": 24,
"aa_end": null,
"aa_length": 101,
"cds_start": 71,
"cds_end": null,
"cds_length": 308,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
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"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "FAM3D",
"gene_hgnc_id": 18665,
"hgvs_c": "n.13+1827G>A",
"hgvs_p": null,
"transcript": "ENST00000482623.5",
"protein_id": "ENSP00000418414.1",
"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": "ENST00000482623.5"
}
],
"gene_symbol": "FAM3D",
"gene_hgnc_id": 18665,
"dbsnp": "rs765250738",
"frequency_reference_population": 0.000051426625,
"hom_count_reference_population": 1,
"allele_count_reference_population": 83,
"gnomad_exomes_af": 0.0000492568,
"gnomad_genomes_af": 0.0000722629,
"gnomad_exomes_ac": 72,
"gnomad_genomes_ac": 11,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0832749605178833,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.23999999463558197,
"splice_prediction_selected": "Uncertain_significance",
"splice_source_selected": "max_spliceai",
"revel_score": 0.045,
"revel_prediction": "Benign",
"alphamissense_score": 0.0943,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.5,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.145,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.24,
"spliceai_max_prediction": "Uncertain_significance",
"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": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_138805.3",
"gene_symbol": "FAM3D",
"hgnc_id": 18665,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.71G>A",
"hgvs_p": "p.Arg24Gln"
}
],
"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
}