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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: 3-171612277-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=171612277&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 171612277,
"ref": "A",
"alt": "G",
"effect": "splice_donor_variant,intron_variant",
"transcript": "NM_002662.5",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 25,
"intron_rank_end": null,
"gene_symbol": "PLD1",
"gene_hgnc_id": 9067,
"hgvs_c": "c.2882+2T>C",
"hgvs_p": null,
"transcript": "NM_002662.5",
"protein_id": "NP_002653.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1074,
"cds_start": null,
"cds_end": null,
"cds_length": 3225,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000351298.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002662.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 25,
"intron_rank_end": null,
"gene_symbol": "PLD1",
"gene_hgnc_id": 9067,
"hgvs_c": "c.2882+2T>C",
"hgvs_p": null,
"transcript": "ENST00000351298.9",
"protein_id": "ENSP00000342793.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1074,
"cds_start": null,
"cds_end": null,
"cds_length": 3225,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002662.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000351298.9"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": 24,
"intron_rank_end": null,
"gene_symbol": "PLD1",
"gene_hgnc_id": 9067,
"hgvs_c": "c.2768+2T>C",
"hgvs_p": null,
"transcript": "ENST00000356327.9",
"protein_id": "ENSP00000348681.5",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1036,
"cds_start": null,
"cds_end": null,
"cds_length": 3111,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000356327.9"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "PLD1",
"gene_hgnc_id": 9067,
"hgvs_c": "c.668+2T>C",
"hgvs_p": null,
"transcript": "ENST00000446289.1",
"protein_id": "ENSP00000395556.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 233,
"cds_start": null,
"cds_end": null,
"cds_length": 702,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000446289.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 25,
"intron_rank_end": null,
"gene_symbol": "PLD1",
"gene_hgnc_id": 9067,
"hgvs_c": "c.2882+2T>C",
"hgvs_p": null,
"transcript": "ENST00000959555.1",
"protein_id": "ENSP00000629614.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1074,
"cds_start": null,
"cds_end": null,
"cds_length": 3225,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000959555.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": 24,
"intron_rank_end": null,
"gene_symbol": "PLD1",
"gene_hgnc_id": 9067,
"hgvs_c": "c.2798+2T>C",
"hgvs_p": null,
"transcript": "ENST00000861048.1",
"protein_id": "ENSP00000531107.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1046,
"cds_start": null,
"cds_end": null,
"cds_length": 3141,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000861048.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": 24,
"intron_rank_end": null,
"gene_symbol": "PLD1",
"gene_hgnc_id": 9067,
"hgvs_c": "c.2768+2T>C",
"hgvs_p": null,
"transcript": "NM_001130081.3",
"protein_id": "NP_001123553.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1036,
"cds_start": null,
"cds_end": null,
"cds_length": 3111,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001130081.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": 24,
"intron_rank_end": null,
"gene_symbol": "PLD1",
"gene_hgnc_id": 9067,
"hgvs_c": "c.2768+2T>C",
"hgvs_p": null,
"transcript": "ENST00000861047.1",
"protein_id": "ENSP00000531106.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1036,
"cds_start": null,
"cds_end": null,
"cds_length": 3111,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000861047.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": 26,
"intron_rank_end": null,
"gene_symbol": "PLD1",
"gene_hgnc_id": 9067,
"hgvs_c": "c.2768+2T>C",
"hgvs_p": null,
"transcript": "ENST00000861051.1",
"protein_id": "ENSP00000531110.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1036,
"cds_start": null,
"cds_end": null,
"cds_length": 3111,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000861051.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 25,
"intron_rank_end": null,
"gene_symbol": "PLD1",
"gene_hgnc_id": 9067,
"hgvs_c": "c.2768+2T>C",
"hgvs_p": null,
"transcript": "ENST00000861052.1",
"protein_id": "ENSP00000531111.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1036,
"cds_start": null,
"cds_end": null,
"cds_length": 3111,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000861052.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": 24,
"intron_rank_end": null,
"gene_symbol": "PLD1",
"gene_hgnc_id": 9067,
"hgvs_c": "c.2768+2T>C",
"hgvs_p": null,
"transcript": "ENST00000861053.1",
"protein_id": "ENSP00000531112.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1036,
"cds_start": null,
"cds_end": null,
"cds_length": 3111,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000861053.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": 24,
"intron_rank_end": null,
"gene_symbol": "PLD1",
"gene_hgnc_id": 9067,
"hgvs_c": "c.2768+2T>C",
"hgvs_p": null,
"transcript": "ENST00000959556.1",
"protein_id": "ENSP00000629615.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1036,
"cds_start": null,
"cds_end": null,
"cds_length": 3111,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000959556.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": 23,
"intron_rank_end": null,
"gene_symbol": "PLD1",
"gene_hgnc_id": 9067,
"hgvs_c": "c.2633+2T>C",
"hgvs_p": null,
"transcript": "ENST00000861049.1",
"protein_id": "ENSP00000531108.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 991,
"cds_start": null,
"cds_end": null,
"cds_length": 2976,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000861049.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": 23,
"intron_rank_end": null,
"gene_symbol": "PLD1",
"gene_hgnc_id": 9067,
"hgvs_c": "c.2618+2T>C",
"hgvs_p": null,
"transcript": "ENST00000861050.1",
"protein_id": "ENSP00000531109.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 986,
"cds_start": null,
"cds_end": null,
"cds_length": 2961,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000861050.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": 22,
"intron_rank_end": null,
"gene_symbol": "PLD1",
"gene_hgnc_id": 9067,
"hgvs_c": "c.2564+2T>C",
"hgvs_p": null,
"transcript": "ENST00000959554.1",
"protein_id": "ENSP00000629613.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 968,
"cds_start": null,
"cds_end": null,
"cds_length": 2907,
"cdna_start": null,
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"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000959554.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 25,
"intron_rank_end": null,
"gene_symbol": "PLD1",
"gene_hgnc_id": 9067,
"hgvs_c": "c.2882+2T>C",
"hgvs_p": null,
"transcript": "XM_005247533.3",
"protein_id": "XP_005247590.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1074,
"cds_start": null,
"cds_end": null,
"cds_length": 3225,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005247533.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 25,
"intron_rank_end": null,
"gene_symbol": "PLD1",
"gene_hgnc_id": 9067,
"hgvs_c": "c.2882+2T>C",
"hgvs_p": null,
"transcript": "XM_047448316.1",
"protein_id": "XP_047304272.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1074,
"cds_start": null,
"cds_end": null,
"cds_length": 3225,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448316.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": 24,
"intron_rank_end": null,
"gene_symbol": "PLD1",
"gene_hgnc_id": 9067,
"hgvs_c": "c.2768+2T>C",
"hgvs_p": null,
"transcript": "XM_005247534.3",
"protein_id": "XP_005247591.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1036,
"cds_start": null,
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"cdna_start": null,
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"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005247534.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": 25,
"intron_rank_end": null,
"gene_symbol": "PLD1",
"gene_hgnc_id": 9067,
"hgvs_c": "c.2882+2T>C",
"hgvs_p": null,
"transcript": "XM_011512897.2",
"protein_id": "XP_011511199.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 971,
"cds_start": null,
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"cds_length": 2916,
"cdna_start": null,
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"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011512897.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 25,
"intron_rank_end": null,
"gene_symbol": "PLD1",
"gene_hgnc_id": 9067,
"hgvs_c": "c.2882+2T>C",
"hgvs_p": null,
"transcript": "XM_011512898.2",
"protein_id": "XP_011511200.1",
"transcript_support_level": null,
"aa_start": null,
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"aa_length": 969,
"cds_start": null,
"cds_end": null,
"cds_length": 2910,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011512898.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": 24,
"intron_rank_end": null,
"gene_symbol": "PLD1",
"gene_hgnc_id": 9067,
"hgvs_c": "c.2768+2T>C",
"hgvs_p": null,
"transcript": "XM_047448317.1",
"protein_id": "XP_047304273.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 933,
"cds_start": null,
"cds_end": null,
"cds_length": 2802,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448317.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "PLD1",
"gene_hgnc_id": 9067,
"hgvs_c": "c.1778+2T>C",
"hgvs_p": null,
"transcript": "XM_047448318.1",
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{
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{
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{
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{
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"biotype": "retained_intron",
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],
"gene_symbol": "PLD1",
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"dbsnp": "rs1085307450",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
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"gnomad_exomes_homalt": null,
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"gnomad_mito_homoplasmic": null,
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"computational_score_selected": 0.20000000298023224,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.6399999856948853,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.2,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.294,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.9,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.98918007292081,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 11,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5",
"acmg_by_gene": [
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PVS1",
"PM2",
"PP5"
],
"verdict": "Pathogenic",
"transcript": "NM_002662.5",
"gene_symbol": "PLD1",
"hgnc_id": 9067,
"effects": [
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"intron_variant"
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"inheritance_mode": "AR",
"hgvs_c": "c.2882+2T>C",
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}
],
"clinvar_disease": " developmental,Cardiac valvular defect",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Cardiac valvular defect, developmental",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}