rs2541669

chr16-172141-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.388

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.340

Gnomad4 FIN AF: 0.480

Gnomad4 NFE AF: 0.443

Gnomad4 OTH AF: 0.368

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

Splicing

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

Publications

LitVar

Other links and lift over

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