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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: 18-7888226-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=18&pos=7888226&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "18",
"pos": 7888226,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_001105244.2",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRM",
"gene_hgnc_id": 9675,
"hgvs_c": "c.317A>G",
"hgvs_p": "p.Lys106Arg",
"transcript": "NM_001105244.2",
"protein_id": "NP_001098714.1",
"transcript_support_level": null,
"aa_start": 106,
"aa_end": null,
"aa_length": 1465,
"cds_start": 317,
"cds_end": null,
"cds_length": 4398,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000580170.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001105244.2"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRM",
"gene_hgnc_id": 9675,
"hgvs_c": "c.317A>G",
"hgvs_p": "p.Lys106Arg",
"transcript": "ENST00000580170.6",
"protein_id": "ENSP00000463325.1",
"transcript_support_level": 1,
"aa_start": 106,
"aa_end": null,
"aa_length": 1465,
"cds_start": 317,
"cds_end": null,
"cds_length": 4398,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001105244.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000580170.6"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRM",
"gene_hgnc_id": 9675,
"hgvs_c": "c.317A>G",
"hgvs_p": "p.Lys106Arg",
"transcript": "ENST00000332175.12",
"protein_id": "ENSP00000331418.8",
"transcript_support_level": 1,
"aa_start": 106,
"aa_end": null,
"aa_length": 1452,
"cds_start": 317,
"cds_end": null,
"cds_length": 4359,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000332175.12"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRM",
"gene_hgnc_id": 9675,
"hgvs_c": "c.317A>G",
"hgvs_p": "p.Lys106Arg",
"transcript": "NM_002845.4",
"protein_id": "NP_002836.3",
"transcript_support_level": null,
"aa_start": 106,
"aa_end": null,
"aa_length": 1452,
"cds_start": 317,
"cds_end": null,
"cds_length": 4359,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002845.4"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRM",
"gene_hgnc_id": 9675,
"hgvs_c": "c.131A>G",
"hgvs_p": "p.Lys44Arg",
"transcript": "ENST00000400053.8",
"protein_id": "ENSP00000382927.4",
"transcript_support_level": 5,
"aa_start": 44,
"aa_end": null,
"aa_length": 1390,
"cds_start": 131,
"cds_end": null,
"cds_length": 4173,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000400053.8"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRM",
"gene_hgnc_id": 9675,
"hgvs_c": "c.392A>G",
"hgvs_p": "p.Lys131Arg",
"transcript": "XM_017025894.2",
"protein_id": "XP_016881383.2",
"transcript_support_level": null,
"aa_start": 131,
"aa_end": null,
"aa_length": 1532,
"cds_start": 392,
"cds_end": null,
"cds_length": 4599,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017025894.2"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRM",
"gene_hgnc_id": 9675,
"hgvs_c": "c.392A>G",
"hgvs_p": "p.Lys131Arg",
"transcript": "XM_017025895.2",
"protein_id": "XP_016881384.2",
"transcript_support_level": null,
"aa_start": 131,
"aa_end": null,
"aa_length": 1528,
"cds_start": 392,
"cds_end": null,
"cds_length": 4587,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017025895.2"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRM",
"gene_hgnc_id": 9675,
"hgvs_c": "c.392A>G",
"hgvs_p": "p.Lys131Arg",
"transcript": "XM_017025896.2",
"protein_id": "XP_016881385.2",
"transcript_support_level": null,
"aa_start": 131,
"aa_end": null,
"aa_length": 1519,
"cds_start": 392,
"cds_end": null,
"cds_length": 4560,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017025896.2"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRM",
"gene_hgnc_id": 9675,
"hgvs_c": "c.392A>G",
"hgvs_p": "p.Lys131Arg",
"transcript": "XM_017025897.2",
"protein_id": "XP_016881386.2",
"transcript_support_level": null,
"aa_start": 131,
"aa_end": null,
"aa_length": 1515,
"cds_start": 392,
"cds_end": null,
"cds_length": 4548,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017025897.2"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRM",
"gene_hgnc_id": 9675,
"hgvs_c": "c.392A>G",
"hgvs_p": "p.Lys131Arg",
"transcript": "XM_017025898.2",
"protein_id": "XP_016881387.2",
"transcript_support_level": null,
"aa_start": 131,
"aa_end": null,
"aa_length": 1511,
"cds_start": 392,
"cds_end": null,
"cds_length": 4536,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017025898.2"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRM",
"gene_hgnc_id": 9675,
"hgvs_c": "c.317A>G",
"hgvs_p": "p.Lys106Arg",
"transcript": "XM_011525708.3",
"protein_id": "XP_011524010.1",
"transcript_support_level": null,
"aa_start": 106,
"aa_end": null,
"aa_length": 1507,
"cds_start": 317,
"cds_end": null,
"cds_length": 4524,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011525708.3"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRM",
"gene_hgnc_id": 9675,
"hgvs_c": "c.392A>G",
"hgvs_p": "p.Lys131Arg",
"transcript": "XM_017025899.2",
"protein_id": "XP_016881388.2",
"transcript_support_level": null,
"aa_start": 131,
"aa_end": null,
"aa_length": 1507,
"cds_start": 392,
"cds_end": null,
"cds_length": 4524,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017025899.2"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRM",
"gene_hgnc_id": 9675,
"hgvs_c": "c.392A>G",
"hgvs_p": "p.Lys131Arg",
"transcript": "XM_017025900.2",
"protein_id": "XP_016881389.2",
"transcript_support_level": null,
"aa_start": 131,
"aa_end": null,
"aa_length": 1502,
"cds_start": 392,
"cds_end": null,
"cds_length": 4509,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017025900.2"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRM",
"gene_hgnc_id": 9675,
"hgvs_c": "c.392A>G",
"hgvs_p": "p.Lys131Arg",
"transcript": "XM_017025901.2",
"protein_id": "XP_016881390.2",
"transcript_support_level": null,
"aa_start": 131,
"aa_end": null,
"aa_length": 1494,
"cds_start": 392,
"cds_end": null,
"cds_length": 4485,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017025901.2"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRM",
"gene_hgnc_id": 9675,
"hgvs_c": "c.392A>G",
"hgvs_p": "p.Lys131Arg",
"transcript": "XM_017025902.2",
"protein_id": "XP_016881391.2",
"transcript_support_level": null,
"aa_start": 131,
"aa_end": null,
"aa_length": 1490,
"cds_start": 392,
"cds_end": null,
"cds_length": 4473,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017025902.2"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRM",
"gene_hgnc_id": 9675,
"hgvs_c": "c.392A>G",
"hgvs_p": "p.Lys131Arg",
"transcript": "XM_017025903.2",
"protein_id": "XP_016881392.2",
"transcript_support_level": null,
"aa_start": 131,
"aa_end": null,
"aa_length": 1486,
"cds_start": 392,
"cds_end": null,
"cds_length": 4461,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017025903.2"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRM",
"gene_hgnc_id": 9675,
"hgvs_c": "c.317A>G",
"hgvs_p": "p.Lys106Arg",
"transcript": "XM_011525712.3",
"protein_id": "XP_011524014.1",
"transcript_support_level": null,
"aa_start": 106,
"aa_end": null,
"aa_length": 1482,
"cds_start": 317,
"cds_end": null,
"cds_length": 4449,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011525712.3"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRM",
"gene_hgnc_id": 9675,
"hgvs_c": "c.317A>G",
"hgvs_p": "p.Lys106Arg",
"transcript": "XM_047437714.1",
"protein_id": "XP_047293670.1",
"transcript_support_level": null,
"aa_start": 106,
"aa_end": null,
"aa_length": 1478,
"cds_start": 317,
"cds_end": null,
"cds_length": 4437,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047437714.1"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRM",
"gene_hgnc_id": 9675,
"hgvs_c": "c.392A>G",
"hgvs_p": "p.Lys131Arg",
"transcript": "XM_017025904.2",
"protein_id": "XP_016881393.2",
"transcript_support_level": null,
"aa_start": 131,
"aa_end": null,
"aa_length": 1477,
"cds_start": 392,
"cds_end": null,
"cds_length": 4434,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017025904.2"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRM",
"gene_hgnc_id": 9675,
"hgvs_c": "c.317A>G",
"hgvs_p": "p.Lys106Arg",
"transcript": "XM_047437715.1",
"protein_id": "XP_047293671.1",
"transcript_support_level": null,
"aa_start": 106,
"aa_end": null,
"aa_length": 1477,
"cds_start": 317,
"cds_end": null,
"cds_length": 4434,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047437715.1"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRM",
"gene_hgnc_id": 9675,
"hgvs_c": "c.317A>G",
"hgvs_p": "p.Lys106Arg",
"transcript": "XM_047437716.1",
"protein_id": "XP_047293672.1",
"transcript_support_level": null,
"aa_start": 106,
"aa_end": null,
"aa_length": 1469,
"cds_start": 317,
"cds_end": null,
"cds_length": 4410,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047437716.1"
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTPRM",
"gene_hgnc_id": 9675,
"hgvs_c": "c.317A>G",
"hgvs_p": "p.Lys106Arg",
"transcript": "XM_047437717.1",
"protein_id": "XP_047293673.1",
"transcript_support_level": null,
"aa_start": 106,
"aa_end": null,
"aa_length": 1461,
"cds_start": 317,
"cds_end": null,
"cds_length": 4386,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
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{
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{
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],
"gene_symbol": "PTPRM",
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"dbsnp": "rs760798931",
"frequency_reference_population": 0.000016108646,
"hom_count_reference_population": 0,
"allele_count_reference_population": 26,
"gnomad_exomes_af": 0.0000171013,
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"gnomad_genomes_ac": 1,
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"gnomad_genomes_homalt": 0,
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"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.03350350260734558,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.3799999952316284,
"splice_prediction_selected": "Uncertain_significance",
"splice_source_selected": "max_spliceai",
"revel_score": 0.148,
"revel_prediction": "Benign",
"alphamissense_score": 0.0726,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.65,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.154,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.38,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BS2",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_001105244.2",
"gene_symbol": "PTPRM",
"hgnc_id": 9675,
"effects": [
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],
"inheritance_mode": "AD",
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],
"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
}