rs2541669

Variant names:

• chr16-172141-C-T
• rs2541669

Variant summary

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

The variant allele was found at a frequency of 0.369 in 145,370 control chromosomes in the GnomAD database, including 10,544 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 0.37 (10544 hom., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.984
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.439 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: 0.370 AC: 53698 AN: 145260 Hom.: 10547 Cov.: 21

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.388

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.369 AC: 53709 AN: 145370 Hom.: 10544 Cov.: 21 AF XY: 0.370 AC XY: 26075 AN XY: 70510

African (AFR) AF: 0.212 AC: 8332 AN: 39342

American (AMR) AF: 0.388 AC: 5570 AN: 14362

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1426 AN: 3388

East Asian (EAS) AF: 0.328 AC: 1547 AN: 4710

South Asian (SAS) AF: 0.340 AC: 1502 AN: 4418

European-Finnish (FIN) AF: 0.480 AC: 4695 AN: 9774

Middle Eastern (MID) AF: 0.400 AC: 116 AN: 290

European-Non Finnish (NFE) AF: 0.443 AC: 29324 AN: 66190

Other (OTH) AF: 0.368 AC: 735 AN: 1996

Alfa AF: 0.404 Hom.: 1450

Bravo AF: 0.361

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.5
DANN	Benign	0.62
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs2541669; hg19: chr16-222140; COSMIC: COSV52406923;