15-59532788-C-T

Variant names:

• chr15-59532788-C-T
• rs17302400
• ENST00000799947.1:n.68-3379C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000799947.1(ENSG00000304125):​n.68-3379C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,174 control chromosomes in the GnomAD database, including 2,768 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.18 (2768 hom., cov: 33)
• Consequence: ENSG00000304125 ENST00000799947.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0380
• Publications: 7 publications found

Genes affected

ENSG00000304125 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304125	ENST00000799947.1	n.68-3379C>T		intron_variant	Intron 1 of 2
ENSG00000304125	ENST00000799948.1	n.63-3379C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27430 AN: 152056 Hom.: 2755 Cov.: 33

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.190

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.181 AC: 27486 AN: 152174 Hom.: 2768 Cov.: 33 AF XY: 0.183 AC XY: 13624 AN XY: 74404

African (AFR) AF: 0.205 AC: 8518 AN: 41526

American (AMR) AF: 0.314 AC: 4805 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 448 AN: 3468

East Asian (EAS) AF: 0.295 AC: 1527 AN: 5182

South Asian (SAS) AF: 0.215 AC: 1035 AN: 4818

European-Finnish (FIN) AF: 0.135 AC: 1428 AN: 10580

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9084 AN: 67998

Other (OTH) AF: 0.192 AC: 405 AN: 2114

Alfa AF: 0.156 Hom.: 5464

Bravo AF: 0.197

Asia WGS AF: 0.271 AC: 940 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.8
DANN	Benign	0.69
PhyloP100		0.038

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs17302400; hg19: chr15-59824987;