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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: 2-203440370-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=203440370&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 203440370,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "ENST00000319170.10",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPH1",
"gene_hgnc_id": 14436,
"hgvs_c": "c.2820A>G",
"hgvs_p": "p.Pro940Pro",
"transcript": "NM_213589.3",
"protein_id": "NP_998754.1",
"transcript_support_level": null,
"aa_start": 940,
"aa_end": null,
"aa_length": 1250,
"cds_start": 2820,
"cds_end": null,
"cds_length": 3753,
"cdna_start": 3011,
"cdna_end": null,
"cdna_length": 9699,
"mane_select": "ENST00000319170.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPH1",
"gene_hgnc_id": 14436,
"hgvs_c": "c.2820A>G",
"hgvs_p": "p.Pro940Pro",
"transcript": "ENST00000319170.10",
"protein_id": "ENSP00000316543.5",
"transcript_support_level": 1,
"aa_start": 940,
"aa_end": null,
"aa_length": 1250,
"cds_start": 2820,
"cds_end": null,
"cds_length": 3753,
"cdna_start": 3011,
"cdna_end": null,
"cdna_length": 9699,
"mane_select": "NM_213589.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABI2",
"gene_hgnc_id": 24011,
"hgvs_c": "c.*13018T>C",
"hgvs_p": null,
"transcript": "ENST00000295851.10",
"protein_id": "ENSP00000295851.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 513,
"cds_start": -4,
"cds_end": null,
"cds_length": 1542,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 22039,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPH1",
"gene_hgnc_id": 14436,
"hgvs_c": "c.2976A>G",
"hgvs_p": "p.Pro992Pro",
"transcript": "NM_001439019.1",
"protein_id": "NP_001425948.1",
"transcript_support_level": null,
"aa_start": 992,
"aa_end": null,
"aa_length": 1302,
"cds_start": 2976,
"cds_end": null,
"cds_length": 3909,
"cdna_start": 3167,
"cdna_end": null,
"cdna_length": 9855,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPH1",
"gene_hgnc_id": 14436,
"hgvs_c": "c.2976A>G",
"hgvs_p": "p.Pro992Pro",
"transcript": "ENST00000374493.7",
"protein_id": "ENSP00000363617.3",
"transcript_support_level": 5,
"aa_start": 992,
"aa_end": null,
"aa_length": 1302,
"cds_start": 2976,
"cds_end": null,
"cds_length": 3909,
"cdna_start": 2976,
"cdna_end": null,
"cdna_length": 3909,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPH1",
"gene_hgnc_id": 14436,
"hgvs_c": "c.2976A>G",
"hgvs_p": "p.Pro992Pro",
"transcript": "ENST00000630330.2",
"protein_id": "ENSP00000486548.1",
"transcript_support_level": 5,
"aa_start": 992,
"aa_end": null,
"aa_length": 1302,
"cds_start": 2976,
"cds_end": null,
"cds_length": 3909,
"cdna_start": 3201,
"cdna_end": null,
"cdna_length": 4134,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPH1",
"gene_hgnc_id": 14436,
"hgvs_c": "c.2901A>G",
"hgvs_p": "p.Pro967Pro",
"transcript": "NM_001439027.1",
"protein_id": "NP_001425956.1",
"transcript_support_level": null,
"aa_start": 967,
"aa_end": null,
"aa_length": 1277,
"cds_start": 2901,
"cds_end": null,
"cds_length": 3834,
"cdna_start": 3092,
"cdna_end": null,
"cdna_length": 9780,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPH1",
"gene_hgnc_id": 14436,
"hgvs_c": "c.2895A>G",
"hgvs_p": "p.Pro965Pro",
"transcript": "NM_001439024.1",
"protein_id": "NP_001425953.1",
"transcript_support_level": null,
"aa_start": 965,
"aa_end": null,
"aa_length": 1275,
"cds_start": 2895,
"cds_end": null,
"cds_length": 3828,
"cdna_start": 3086,
"cdna_end": null,
"cdna_length": 9774,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPH1",
"gene_hgnc_id": 14436,
"hgvs_c": "c.2895A>G",
"hgvs_p": "p.Pro965Pro",
"transcript": "NM_001439030.1",
"protein_id": "NP_001425959.1",
"transcript_support_level": null,
"aa_start": 965,
"aa_end": null,
"aa_length": 1275,
"cds_start": 2895,
"cds_end": null,
"cds_length": 3828,
"cdna_start": 3167,
"cdna_end": null,
"cdna_length": 9855,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPH1",
"gene_hgnc_id": 14436,
"hgvs_c": "c.2820A>G",
"hgvs_p": "p.Pro940Pro",
"transcript": "NM_001439031.1",
"protein_id": "NP_001425960.1",
"transcript_support_level": null,
"aa_start": 940,
"aa_end": null,
"aa_length": 1250,
"cds_start": 2820,
"cds_end": null,
"cds_length": 3753,
"cdna_start": 3092,
"cdna_end": null,
"cdna_length": 9780,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPH1",
"gene_hgnc_id": 14436,
"hgvs_c": "c.3048A>G",
"hgvs_p": "p.Pro1016Pro",
"transcript": "XM_047445538.1",
"protein_id": "XP_047301494.1",
"transcript_support_level": null,
"aa_start": 1016,
"aa_end": null,
"aa_length": 1326,
"cds_start": 3048,
"cds_end": null,
"cds_length": 3981,
"cdna_start": 3071,
"cdna_end": null,
"cdna_length": 9759,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPH1",
"gene_hgnc_id": 14436,
"hgvs_c": "c.2976A>G",
"hgvs_p": "p.Pro992Pro",
"transcript": "XM_006712695.4",
"protein_id": "XP_006712758.1",
"transcript_support_level": null,
"aa_start": 992,
"aa_end": null,
"aa_length": 1302,
"cds_start": 2976,
"cds_end": null,
"cds_length": 3909,
"cdna_start": 3924,
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"cdna_length": 10612,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPH1",
"gene_hgnc_id": 14436,
"hgvs_c": "c.2976A>G",
"hgvs_p": "p.Pro992Pro",
"transcript": "XM_011511646.4",
"protein_id": "XP_011509948.1",
"transcript_support_level": null,
"aa_start": 992,
"aa_end": null,
"aa_length": 1302,
"cds_start": 2976,
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"cds_length": 3909,
"cdna_start": 3248,
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"cdna_length": 9936,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
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"gene_symbol": "RAPH1",
"gene_hgnc_id": 14436,
"hgvs_c": "c.2976A>G",
"hgvs_p": "p.Pro992Pro",
"transcript": "XM_047445539.1",
"protein_id": "XP_047301495.1",
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"cds_start": 2976,
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"cdna_start": 3371,
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"cdna_length": 10059,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPH1",
"gene_hgnc_id": 14436,
"hgvs_c": "c.2976A>G",
"hgvs_p": "p.Pro992Pro",
"transcript": "XM_047445540.1",
"protein_id": "XP_047301496.1",
"transcript_support_level": null,
"aa_start": 992,
"aa_end": null,
"aa_length": 1302,
"cds_start": 2976,
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"cdna_start": 3152,
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"cdna_length": 9840,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
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"gene_symbol": "RAPH1",
"gene_hgnc_id": 14436,
"hgvs_c": "c.2976A>G",
"hgvs_p": "p.Pro992Pro",
"transcript": "XM_047445541.1",
"protein_id": "XP_047301497.1",
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"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPH1",
"gene_hgnc_id": 14436,
"hgvs_c": "c.2973A>G",
"hgvs_p": "p.Pro991Pro",
"transcript": "XM_047445542.1",
"protein_id": "XP_047301498.1",
"transcript_support_level": null,
"aa_start": 991,
"aa_end": null,
"aa_length": 1301,
"cds_start": 2973,
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"cds_length": 3906,
"cdna_start": 2996,
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"cdna_length": 9684,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPH1",
"gene_hgnc_id": 14436,
"hgvs_c": "c.2967A>G",
"hgvs_p": "p.Pro989Pro",
"transcript": "XM_047445543.1",
"protein_id": "XP_047301499.1",
"transcript_support_level": null,
"aa_start": 989,
"aa_end": null,
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"cds_start": 2967,
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"cdna_start": 2990,
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
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"gene_symbol": "RAPH1",
"gene_hgnc_id": 14436,
"hgvs_c": "c.2892A>G",
"hgvs_p": "p.Pro964Pro",
"transcript": "XM_047445547.1",
"protein_id": "XP_047301503.1",
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"feature": null
},
{
"aa_ref": "P",
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"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RAPH1",
"gene_hgnc_id": 14436,
"hgvs_c": "c.1416A>G",
"hgvs_p": "p.Pro472Pro",
"transcript": "XM_047445549.1",
"protein_id": "XP_047301505.1",
"transcript_support_level": null,
"aa_start": 472,
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"cds_start": 1416,
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"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
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"exon_count": 14,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "RAPH1",
"gene_hgnc_id": 14436,
"hgvs_c": "c.1776+4498A>G",
"hgvs_p": null,
"transcript": "ENST00000457812.5",
"protein_id": "ENSP00000392854.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 594,
"cds_start": -4,
"cds_end": null,
"cds_length": 1785,
"cdna_start": null,
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"cdna_length": 2673,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RAPH1",
"gene_hgnc_id": 14436,
"dbsnp": "rs3814365",
"frequency_reference_population": 0.54191256,
"hom_count_reference_population": 236589,
"allele_count_reference_population": 855319,
"gnomad_exomes_af": 0.54923,
"gnomad_genomes_af": 0.468835,
"gnomad_exomes_ac": 787968,
"gnomad_genomes_ac": 67351,
"gnomad_exomes_homalt": 219553,
"gnomad_genomes_homalt": 17036,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.9399999976158142,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.94,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -3.591,
"phylop100way_prediction": "Benign",
"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": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000319170.10",
"gene_symbol": "RAPH1",
"hgnc_id": 14436,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2820A>G",
"hgvs_p": "p.Pro940Pro"
},
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000295851.10",
"gene_symbol": "ABI2",
"hgnc_id": 24011,
"effects": [
"3_prime_UTR_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.*13018T>C",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}