15-60341477-A-C

Variant names:

• chr15-60341477-A-C
• rs7169359

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.201 AC: 8331 AN: 41496

American (AMR) AF: 0.0924 AC: 1413 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 531 AN: 3470

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5188

South Asian (SAS) AF: 0.0314 AC: 151 AN: 4814

European-Finnish (FIN) AF: 0.0796 AC: 844 AN: 10600

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8298 AN: 67994

Other (OTH) AF: 0.122 AC: 258 AN: 2112

Alfa AF: 0.120 Hom.: 619

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
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs7169359; hg19: chr15-60633676;