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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: 19-3633466-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=3633466&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 3633466,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_012398.3",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIP5K1C",
"gene_hgnc_id": 8996,
"hgvs_c": "c.1975C>T",
"hgvs_p": "p.Pro659Ser",
"transcript": "NM_012398.3",
"protein_id": "NP_036530.1",
"transcript_support_level": null,
"aa_start": 659,
"aa_end": null,
"aa_length": 668,
"cds_start": 1975,
"cds_end": null,
"cds_length": 2007,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000335312.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_012398.3"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIP5K1C",
"gene_hgnc_id": 8996,
"hgvs_c": "c.1975C>T",
"hgvs_p": "p.Pro659Ser",
"transcript": "ENST00000335312.8",
"protein_id": "ENSP00000335333.3",
"transcript_support_level": 1,
"aa_start": 659,
"aa_end": null,
"aa_length": 668,
"cds_start": 1975,
"cds_end": null,
"cds_length": 2007,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_012398.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000335312.8"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIP5K1C",
"gene_hgnc_id": 8996,
"hgvs_c": "c.2092C>T",
"hgvs_p": "p.Pro698Ser",
"transcript": "ENST00000876625.1",
"protein_id": "ENSP00000546684.1",
"transcript_support_level": null,
"aa_start": 698,
"aa_end": null,
"aa_length": 707,
"cds_start": 2092,
"cds_end": null,
"cds_length": 2124,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000876625.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIP5K1C",
"gene_hgnc_id": 8996,
"hgvs_c": "c.2077C>T",
"hgvs_p": "p.Pro693Ser",
"transcript": "ENST00000967141.1",
"protein_id": "ENSP00000637200.1",
"transcript_support_level": null,
"aa_start": 693,
"aa_end": null,
"aa_length": 702,
"cds_start": 2077,
"cds_end": null,
"cds_length": 2109,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000967141.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIP5K1C",
"gene_hgnc_id": 8996,
"hgvs_c": "c.2053C>T",
"hgvs_p": "p.Pro685Ser",
"transcript": "ENST00000679885.1",
"protein_id": "ENSP00000504894.1",
"transcript_support_level": null,
"aa_start": 685,
"aa_end": null,
"aa_length": 694,
"cds_start": 2053,
"cds_end": null,
"cds_length": 2085,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000679885.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIP5K1C",
"gene_hgnc_id": 8996,
"hgvs_c": "c.1969C>T",
"hgvs_p": "p.Pro657Ser",
"transcript": "ENST00000876630.1",
"protein_id": "ENSP00000546689.1",
"transcript_support_level": null,
"aa_start": 657,
"aa_end": null,
"aa_length": 666,
"cds_start": 1969,
"cds_end": null,
"cds_length": 2001,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000876630.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIP5K1C",
"gene_hgnc_id": 8996,
"hgvs_c": "c.1963C>T",
"hgvs_p": "p.Pro655Ser",
"transcript": "ENST00000876628.1",
"protein_id": "ENSP00000546687.1",
"transcript_support_level": null,
"aa_start": 655,
"aa_end": null,
"aa_length": 664,
"cds_start": 1963,
"cds_end": null,
"cds_length": 1995,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000876628.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIP5K1C",
"gene_hgnc_id": 8996,
"hgvs_c": "c.1942C>T",
"hgvs_p": "p.Pro648Ser",
"transcript": "ENST00000876622.1",
"protein_id": "ENSP00000546681.1",
"transcript_support_level": null,
"aa_start": 648,
"aa_end": null,
"aa_length": 657,
"cds_start": 1942,
"cds_end": null,
"cds_length": 1974,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000876622.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIP5K1C",
"gene_hgnc_id": 8996,
"hgvs_c": "c.1891C>T",
"hgvs_p": "p.Pro631Ser",
"transcript": "ENST00000876621.1",
"protein_id": "ENSP00000546680.1",
"transcript_support_level": null,
"aa_start": 631,
"aa_end": null,
"aa_length": 640,
"cds_start": 1891,
"cds_end": null,
"cds_length": 1923,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000876621.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIP5K1C",
"gene_hgnc_id": 8996,
"hgvs_c": "c.1882C>T",
"hgvs_p": "p.Pro628Ser",
"transcript": "ENST00000967140.1",
"protein_id": "ENSP00000637199.1",
"transcript_support_level": null,
"aa_start": 628,
"aa_end": null,
"aa_length": 637,
"cds_start": 1882,
"cds_end": null,
"cds_length": 1914,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000967140.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIP5K1C",
"gene_hgnc_id": 8996,
"hgvs_c": "c.1822C>T",
"hgvs_p": "p.Pro608Ser",
"transcript": "ENST00000876629.1",
"protein_id": "ENSP00000546688.1",
"transcript_support_level": null,
"aa_start": 608,
"aa_end": null,
"aa_length": 617,
"cds_start": 1822,
"cds_end": null,
"cds_length": 1854,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000876629.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIP5K1C",
"gene_hgnc_id": 8996,
"hgvs_c": "c.1942C>T",
"hgvs_p": "p.Pro648Ser",
"transcript": "XM_017026540.3",
"protein_id": "XP_016882029.1",
"transcript_support_level": null,
"aa_start": 648,
"aa_end": null,
"aa_length": 657,
"cds_start": 1942,
"cds_end": null,
"cds_length": 1974,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017026540.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIP5K1C",
"gene_hgnc_id": 8996,
"hgvs_c": "c.*119C>T",
"hgvs_p": null,
"transcript": "XM_011527848.2",
"protein_id": "XP_011526150.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 672,
"cds_start": null,
"cds_end": null,
"cds_length": 2019,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011527848.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PIP5K1C",
"gene_hgnc_id": 8996,
"hgvs_c": "c.*119C>T",
"hgvs_p": null,
"transcript": "XM_011527849.2",
"protein_id": "XP_011526151.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 646,
"cds_start": null,
"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": "XM_011527849.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "PIP5K1C",
"gene_hgnc_id": 8996,
"hgvs_c": "c.2071-297C>T",
"hgvs_p": null,
"transcript": "ENST00000918776.1",
"protein_id": "ENSP00000588835.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 690,
"cds_start": null,
"cds_end": null,
"cds_length": 2073,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000918776.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "PIP5K1C",
"gene_hgnc_id": 8996,
"hgvs_c": "c.2053-297C>T",
"hgvs_p": null,
"transcript": "ENST00000918774.1",
"protein_id": "ENSP00000588833.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 684,
"cds_start": null,
"cds_end": null,
"cds_length": 2055,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000918774.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "PIP5K1C",
"gene_hgnc_id": 8996,
"hgvs_c": "c.2023-297C>T",
"hgvs_p": null,
"transcript": "ENST00000876619.1",
"protein_id": "ENSP00000546678.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 674,
"cds_start": null,
"cds_end": null,
"cds_length": 2025,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000876619.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "PIP5K1C",
"gene_hgnc_id": 8996,
"hgvs_c": "c.1999-297C>T",
"hgvs_p": null,
"transcript": "ENST00000876624.1",
"protein_id": "ENSP00000546683.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 666,
"cds_start": null,
"cds_end": null,
"cds_length": 2001,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000876624.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 15,
"intron_rank_end": null,
"gene_symbol": "PIP5K1C",
"gene_hgnc_id": 8996,
"hgvs_c": "c.1990-297C>T",
"hgvs_p": null,
"transcript": "ENST00000918775.1",
"protein_id": "ENSP00000588834.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 663,
"cds_start": null,
"cds_end": null,
"cds_length": 1992,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000918775.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "PIP5K1C",
"gene_hgnc_id": 8996,
"hgvs_c": "c.1921-297C>T",
"hgvs_p": null,
"transcript": "NM_001195733.2",
"protein_id": "NP_001182662.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 640,
"cds_start": null,
"cds_end": null,
"cds_length": 1923,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001195733.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "PIP5K1C",
"gene_hgnc_id": 8996,
"hgvs_c": "c.1921-297C>T",
"hgvs_p": null,
"transcript": "ENST00000539785.5",
"protein_id": "ENSP00000445992.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 640,
"cds_start": null,
"cds_end": null,
"cds_length": 1923,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000539785.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "PIP5K1C",
"gene_hgnc_id": 8996,
"hgvs_c": "c.1915-297C>T",
"hgvs_p": null,
"transcript": "ENST00000876626.1",
"protein_id": "ENSP00000546685.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 638,
"cds_start": null,
"cds_end": null,
"cds_length": 1917,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
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{
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{
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],
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],
"gene_symbol": "PIP5K1C",
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"dbsnp": "rs34633286",
"frequency_reference_population": 0.0060433834,
"hom_count_reference_population": 37,
"allele_count_reference_population": 9117,
"gnomad_exomes_af": 0.00630928,
"gnomad_genomes_af": 0.00367608,
"gnomad_exomes_ac": 8557,
"gnomad_genomes_ac": 560,
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"gnomad_genomes_homalt": 2,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0067649781703948975,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.031,
"revel_prediction": "Benign",
"alphamissense_score": 0.0624,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.58,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.108,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.01,
"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": -16,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS2",
"acmg_by_gene": [
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_012398.3",
"gene_symbol": "PIP5K1C",
"hgnc_id": 8996,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.1975C>T",
"hgvs_p": "p.Pro659Ser"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}