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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: 17-7236560-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=7236560&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 7236560,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_024297.3",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF23",
"gene_hgnc_id": 28428,
"hgvs_c": "c.367G>A",
"hgvs_p": "p.Asp123Asn",
"transcript": "NM_024297.3",
"protein_id": "NP_077273.2",
"transcript_support_level": null,
"aa_start": 123,
"aa_end": null,
"aa_length": 403,
"cds_start": 367,
"cds_end": null,
"cds_length": 1212,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000320316.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_024297.3"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF23",
"gene_hgnc_id": 28428,
"hgvs_c": "c.367G>A",
"hgvs_p": "p.Asp123Asn",
"transcript": "ENST00000320316.8",
"protein_id": "ENSP00000322579.3",
"transcript_support_level": 1,
"aa_start": 123,
"aa_end": null,
"aa_length": 403,
"cds_start": 367,
"cds_end": null,
"cds_length": 1212,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_024297.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000320316.8"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF23",
"gene_hgnc_id": 28428,
"hgvs_c": "c.355G>A",
"hgvs_p": "p.Asp119Asn",
"transcript": "NM_001284518.2",
"protein_id": "NP_001271447.1",
"transcript_support_level": null,
"aa_start": 119,
"aa_end": null,
"aa_length": 399,
"cds_start": 355,
"cds_end": null,
"cds_length": 1200,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001284518.2"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF23",
"gene_hgnc_id": 28428,
"hgvs_c": "c.355G>A",
"hgvs_p": "p.Asp119Asn",
"transcript": "ENST00000454255.6",
"protein_id": "ENSP00000414607.2",
"transcript_support_level": 2,
"aa_start": 119,
"aa_end": null,
"aa_length": 399,
"cds_start": 355,
"cds_end": null,
"cds_length": 1200,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000454255.6"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF23",
"gene_hgnc_id": 28428,
"hgvs_c": "c.166G>A",
"hgvs_p": "p.Asp56Asn",
"transcript": "NM_001284517.2",
"protein_id": "NP_001271446.1",
"transcript_support_level": null,
"aa_start": 56,
"aa_end": null,
"aa_length": 336,
"cds_start": 166,
"cds_end": null,
"cds_length": 1011,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001284517.2"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF23",
"gene_hgnc_id": 28428,
"hgvs_c": "c.166G>A",
"hgvs_p": "p.Asp56Asn",
"transcript": "ENST00000571362.5",
"protein_id": "ENSP00000460738.1",
"transcript_support_level": 2,
"aa_start": 56,
"aa_end": null,
"aa_length": 336,
"cds_start": 166,
"cds_end": null,
"cds_length": 1011,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000571362.5"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF23",
"gene_hgnc_id": 28428,
"hgvs_c": "c.340G>A",
"hgvs_p": "p.Asp114Asn",
"transcript": "ENST00000573826.5",
"protein_id": "ENSP00000461442.1",
"transcript_support_level": 3,
"aa_start": 114,
"aa_end": null,
"aa_length": 202,
"cds_start": 340,
"cds_end": null,
"cds_length": 610,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000573826.5"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF23",
"gene_hgnc_id": 28428,
"hgvs_c": "c.379G>A",
"hgvs_p": "p.Asp127Asn",
"transcript": "ENST00000570899.1",
"protein_id": "ENSP00000458416.1",
"transcript_support_level": 3,
"aa_start": 127,
"aa_end": null,
"aa_length": 185,
"cds_start": 379,
"cds_end": null,
"cds_length": 558,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000570899.1"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF23",
"gene_hgnc_id": 28428,
"hgvs_c": "c.367G>A",
"hgvs_p": "p.Asp123Asn",
"transcript": "ENST00000613632.4",
"protein_id": "ENSP00000479592.1",
"transcript_support_level": 5,
"aa_start": 123,
"aa_end": null,
"aa_length": 158,
"cds_start": 367,
"cds_end": null,
"cds_length": 477,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000613632.4"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF23",
"gene_hgnc_id": 28428,
"hgvs_c": "c.379G>A",
"hgvs_p": "p.Asp127Asn",
"transcript": "XM_024450938.2",
"protein_id": "XP_024306706.1",
"transcript_support_level": null,
"aa_start": 127,
"aa_end": null,
"aa_length": 407,
"cds_start": 379,
"cds_end": null,
"cds_length": 1224,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024450938.2"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF23",
"gene_hgnc_id": 28428,
"hgvs_c": "c.178G>A",
"hgvs_p": "p.Asp60Asn",
"transcript": "XM_047436728.1",
"protein_id": "XP_047292684.1",
"transcript_support_level": null,
"aa_start": 60,
"aa_end": null,
"aa_length": 340,
"cds_start": 178,
"cds_end": null,
"cds_length": 1023,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047436728.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF23",
"gene_hgnc_id": 28428,
"hgvs_c": "c.-24G>A",
"hgvs_p": null,
"transcript": "ENST00000576955.5",
"protein_id": "ENSP00000458953.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 273,
"cds_start": null,
"cds_end": null,
"cds_length": 822,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000576955.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF23",
"gene_hgnc_id": 28428,
"hgvs_c": "c.-24G>A",
"hgvs_p": null,
"transcript": "ENST00000572789.5",
"protein_id": "ENSP00000460876.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 200,
"cds_start": null,
"cds_end": null,
"cds_length": 603,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000572789.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF23",
"gene_hgnc_id": 28428,
"hgvs_c": "c.-24G>A",
"hgvs_p": null,
"transcript": "ENST00000574323.5",
"protein_id": "ENSP00000459983.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 58,
"cds_start": null,
"cds_end": null,
"cds_length": 178,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000574323.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF23",
"gene_hgnc_id": 28428,
"hgvs_c": "c.-24G>A",
"hgvs_p": null,
"transcript": "ENST00000574236.5",
"protein_id": "ENSP00000458401.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 35,
"cds_start": null,
"cds_end": null,
"cds_length": 108,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000574236.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF23",
"gene_hgnc_id": 28428,
"hgvs_c": "c.-24G>A",
"hgvs_p": null,
"transcript": "ENST00000574407.5",
"protein_id": "ENSP00000459904.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 5,
"cds_start": null,
"cds_end": null,
"cds_length": 18,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000574407.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF23",
"gene_hgnc_id": 28428,
"hgvs_c": "c.-24G>A",
"hgvs_p": null,
"transcript": "XM_024450939.2",
"protein_id": "XP_024306707.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 273,
"cds_start": null,
"cds_end": null,
"cds_length": 822,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024450939.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF23",
"gene_hgnc_id": 28428,
"hgvs_c": "c.-24G>A",
"hgvs_p": null,
"transcript": "XM_024450940.2",
"protein_id": "XP_024306708.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 273,
"cds_start": null,
"cds_end": null,
"cds_length": 822,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024450940.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF23",
"gene_hgnc_id": 28428,
"hgvs_c": "c.-24G>A",
"hgvs_p": null,
"transcript": "XM_024450942.2",
"protein_id": "XP_024306710.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 273,
"cds_start": null,
"cds_end": null,
"cds_length": 822,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024450942.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF23",
"gene_hgnc_id": 28428,
"hgvs_c": "c.-24G>A",
"hgvs_p": null,
"transcript": "XM_047436729.1",
"protein_id": "XP_047292685.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 273,
"cds_start": null,
"cds_end": null,
"cds_length": 822,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047436729.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF23",
"gene_hgnc_id": 28428,
"hgvs_c": "c.-24G>A",
"hgvs_p": null,
"transcript": "XM_047436730.1",
"protein_id": "XP_047292686.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 273,
"cds_start": null,
"cds_end": null,
"cds_length": 822,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047436730.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF23",
"gene_hgnc_id": 28428,
"hgvs_c": "n.*57G>A",
"hgvs_p": null,
"transcript": "ENST00000570753.5",
"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": "pseudogene",
"feature": "ENST00000570753.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PHF23",
"gene_hgnc_id": 28428,
"hgvs_c": "n.*77G>A",
"hgvs_p": null,
"transcript": "ENST00000574899.1",
"protein_id": null,
"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": "pseudogene",
"feature": "ENST00000574899.1"
}
],
"gene_symbol": "PHF23",
"gene_hgnc_id": 28428,
"dbsnp": "rs763497608",
"frequency_reference_population": 0.000013630427,
"hom_count_reference_population": 0,
"allele_count_reference_population": 22,
"gnomad_exomes_af": 0.000013681,
"gnomad_genomes_af": 0.0000131447,
"gnomad_exomes_ac": 20,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.23861786723136902,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.147,
"revel_prediction": "Benign",
"alphamissense_score": 0.2029,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.53,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.088,
"phylop100way_prediction": "Uncertain_significance",
"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": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_024297.3",
"gene_symbol": "PHF23",
"hgnc_id": 28428,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.367G>A",
"hgvs_p": "p.Asp123Asn"
}
],
"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
}