rs7169359

chr15-60341477-A-Cchr15-60341477-A-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.131 in 152,172 control chromosomes in the GnomAD database, including 1,526 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 0.13 (1526 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19907 AN: 152054 Hom.: 1523 Cov.: 32

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.0925

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0313

Gnomad FIN AF: 0.0796

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.131 AC: 19935 AN: 152172 Hom.: 1526 Cov.: 32 AF XY: 0.126 AC XY: 9362 AN XY: 74390

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.0924

Gnomad4 ASJ AF: 0.153

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.0314

Gnomad4 FIN AF: 0.0796

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.122

Alfa AF: 0.119 Hom.: 538

Bravo AF: 0.135

Asia WGS AF: 0.0310 AC: 109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
Cadd	Benign	13
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7169359; hg19: chr15-60633676;