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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: 3-183829707-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=183829707&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 183829707,
"ref": "C",
"alt": "A",
"effect": "missense_variant,splice_region_variant",
"transcript": "NM_018622.7",
"consequences": [
{
"aa_ref": "W",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARL",
"gene_hgnc_id": 18253,
"hgvs_c": "c.1031G>T",
"hgvs_p": "p.Trp344Leu",
"transcript": "NM_018622.7",
"protein_id": "NP_061092.3",
"transcript_support_level": null,
"aa_start": 344,
"aa_end": null,
"aa_length": 379,
"cds_start": 1031,
"cds_end": null,
"cds_length": 1140,
"cdna_start": 1065,
"cdna_end": null,
"cdna_length": 1501,
"mane_select": "ENST00000317096.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARL",
"gene_hgnc_id": 18253,
"hgvs_c": "c.1031G>T",
"hgvs_p": "p.Trp344Leu",
"transcript": "ENST00000317096.9",
"protein_id": "ENSP00000325421.5",
"transcript_support_level": 1,
"aa_start": 344,
"aa_end": null,
"aa_length": 379,
"cds_start": 1031,
"cds_end": null,
"cds_length": 1140,
"cdna_start": 1065,
"cdna_end": null,
"cdna_length": 1501,
"mane_select": "NM_018622.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARL",
"gene_hgnc_id": 18253,
"hgvs_c": "c.881G>T",
"hgvs_p": "p.Trp294Leu",
"transcript": "ENST00000311101.9",
"protein_id": "ENSP00000310676.5",
"transcript_support_level": 1,
"aa_start": 294,
"aa_end": null,
"aa_length": 329,
"cds_start": 881,
"cds_end": null,
"cds_length": 990,
"cdna_start": 923,
"cdna_end": null,
"cdna_length": 1240,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "ENSG00000283765",
"gene_hgnc_id": null,
"hgvs_c": "c.1028+3785G>T",
"hgvs_p": null,
"transcript": "ENST00000639401.1",
"protein_id": "ENSP00000491227.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 408,
"cds_start": -4,
"cds_end": null,
"cds_length": 1227,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3058,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARL",
"gene_hgnc_id": 18253,
"hgvs_c": "c.929G>T",
"hgvs_p": "p.Trp310Leu",
"transcript": "NM_001324436.2",
"protein_id": "NP_001311365.1",
"transcript_support_level": null,
"aa_start": 310,
"aa_end": null,
"aa_length": 345,
"cds_start": 929,
"cds_end": null,
"cds_length": 1038,
"cdna_start": 963,
"cdna_end": null,
"cdna_length": 1399,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARL",
"gene_hgnc_id": 18253,
"hgvs_c": "c.881G>T",
"hgvs_p": "p.Trp294Leu",
"transcript": "NM_001037639.3",
"protein_id": "NP_001032728.1",
"transcript_support_level": null,
"aa_start": 294,
"aa_end": null,
"aa_length": 329,
"cds_start": 881,
"cds_end": null,
"cds_length": 990,
"cdna_start": 915,
"cdna_end": null,
"cdna_length": 1351,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARL",
"gene_hgnc_id": 18253,
"hgvs_c": "c.779G>T",
"hgvs_p": "p.Trp260Leu",
"transcript": "NM_001324437.2",
"protein_id": "NP_001311366.1",
"transcript_support_level": null,
"aa_start": 260,
"aa_end": null,
"aa_length": 295,
"cds_start": 779,
"cds_end": null,
"cds_length": 888,
"cdna_start": 813,
"cdna_end": null,
"cdna_length": 1249,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARL",
"gene_hgnc_id": 18253,
"hgvs_c": "c.779G>T",
"hgvs_p": "p.Trp260Leu",
"transcript": "ENST00000435888.5",
"protein_id": "ENSP00000402137.1",
"transcript_support_level": 5,
"aa_start": 260,
"aa_end": null,
"aa_length": 295,
"cds_start": 779,
"cds_end": null,
"cds_length": 888,
"cdna_start": 788,
"cdna_end": null,
"cdna_length": 1098,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARL",
"gene_hgnc_id": 18253,
"hgvs_c": "c.831G>T",
"hgvs_p": "p.Met277Ile",
"transcript": "NM_001324438.2",
"protein_id": "NP_001311367.1",
"transcript_support_level": null,
"aa_start": 277,
"aa_end": null,
"aa_length": 283,
"cds_start": 831,
"cds_end": null,
"cds_length": 852,
"cdna_start": 865,
"cdna_end": null,
"cdna_length": 1301,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARL",
"gene_hgnc_id": 18253,
"hgvs_c": "c.458G>T",
"hgvs_p": "p.Trp153Leu",
"transcript": "ENST00000639100.1",
"protein_id": "ENSP00000491186.1",
"transcript_support_level": 5,
"aa_start": 153,
"aa_end": null,
"aa_length": 188,
"cds_start": 458,
"cds_end": null,
"cds_length": 567,
"cdna_start": 1077,
"cdna_end": null,
"cdna_length": 1513,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARL",
"gene_hgnc_id": 18253,
"hgvs_c": "c.404G>T",
"hgvs_p": "p.Trp135Leu",
"transcript": "ENST00000417784.5",
"protein_id": "ENSP00000398043.1",
"transcript_support_level": 3,
"aa_start": 135,
"aa_end": null,
"aa_length": 170,
"cds_start": 404,
"cds_end": null,
"cds_length": 513,
"cdna_start": 405,
"cdna_end": null,
"cdna_length": 722,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARL",
"gene_hgnc_id": 18253,
"hgvs_c": "c.227G>T",
"hgvs_p": "p.Trp76Leu",
"transcript": "ENST00000418450.5",
"protein_id": "ENSP00000392926.1",
"transcript_support_level": 3,
"aa_start": 76,
"aa_end": null,
"aa_length": 111,
"cds_start": 227,
"cds_end": null,
"cds_length": 336,
"cdna_start": 229,
"cdna_end": null,
"cdna_length": 546,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARL",
"gene_hgnc_id": 18253,
"hgvs_c": "c.171G>T",
"hgvs_p": "p.Met57Ile",
"transcript": "ENST00000450375.5",
"protein_id": "ENSP00000402689.1",
"transcript_support_level": 2,
"aa_start": 57,
"aa_end": null,
"aa_length": 63,
"cds_start": 171,
"cds_end": null,
"cds_length": 192,
"cdna_start": 171,
"cdna_end": null,
"cdna_length": 488,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARL",
"gene_hgnc_id": 18253,
"hgvs_c": "n.*565G>T",
"hgvs_p": null,
"transcript": "ENST00000421484.5",
"protein_id": "ENSP00000404421.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1347,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARL",
"gene_hgnc_id": 18253,
"hgvs_c": "n.*617G>T",
"hgvs_p": null,
"transcript": "ENST00000638817.1",
"protein_id": "ENSP00000492596.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1534,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARL",
"gene_hgnc_id": 18253,
"hgvs_c": "n.*685G>T",
"hgvs_p": null,
"transcript": "ENST00000639900.1",
"protein_id": "ENSP00000491109.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1545,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARL",
"gene_hgnc_id": 18253,
"hgvs_c": "n.1121G>T",
"hgvs_p": null,
"transcript": "NR_136893.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1557,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARL",
"gene_hgnc_id": 18253,
"hgvs_c": "n.*565G>T",
"hgvs_p": null,
"transcript": "ENST00000421484.5",
"protein_id": "ENSP00000404421.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1347,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARL",
"gene_hgnc_id": 18253,
"hgvs_c": "n.*617G>T",
"hgvs_p": null,
"transcript": "ENST00000638817.1",
"protein_id": "ENSP00000492596.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1534,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARL",
"gene_hgnc_id": 18253,
"hgvs_c": "n.*685G>T",
"hgvs_p": null,
"transcript": "ENST00000639900.1",
"protein_id": "ENSP00000491109.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1545,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 10,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "PARL",
"gene_hgnc_id": 18253,
"hgvs_c": "c.1029-2975G>T",
"hgvs_p": null,
"transcript": "XM_005247582.6",
"protein_id": "XP_005247639.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 394,
"cds_start": -4,
"cds_end": null,
"cds_length": 1185,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1306,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 9,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "PARL",
"gene_hgnc_id": 18253,
"hgvs_c": "c.927-2975G>T",
"hgvs_p": null,
"transcript": "XM_017006800.3",
"protein_id": "XP_016862289.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 360,
"cds_start": -4,
"cds_end": null,
"cds_length": 1083,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1204,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 9,
"intron_rank": 8,
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{
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},
{
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],
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}
],
"gene_symbol": "PARL",
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"dbsnp": "rs374252729",
"frequency_reference_population": 0.00004028175,
"hom_count_reference_population": 0,
"allele_count_reference_population": 65,
"gnomad_exomes_af": 0.0000410538,
"gnomad_genomes_af": 0.0000328653,
"gnomad_exomes_ac": 60,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.2686837911605835,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.3,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.4249,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": 0.01,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.565,
"phylop100way_prediction": "Pathogenic",
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_018622.7",
"gene_symbol": "PARL",
"hgnc_id": 18253,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1031G>T",
"hgvs_p": "p.Trp344Leu"
},
{
"score": 1,
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"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000639401.1",
"gene_symbol": "ENSG00000283765",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1028+3785G>T",
"hgvs_p": null
}
],
"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
}