rs10852344

Variant names:

• chr16-11923062-C-T
• rs10852344

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 0.425 in 151,716 control chromosomes in the GnomAD database, including 16,559 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 0.43 (16559 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650
• Publications: 37 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.578 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: 0.426 AC: 64528 AN: 151598 Hom.: 16564 Cov.: 30

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.594

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.485

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

GnomAD4 genome AF: 0.425 AC: 64523 AN: 151716 Hom.: 16559 Cov.: 30 AF XY: 0.419 AC XY: 31072 AN XY: 74116

African (AFR) AF: 0.156 AC: 6435 AN: 41378

American (AMR) AF: 0.481 AC: 7313 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1854 AN: 3466

East Asian (EAS) AF: 0.179 AC: 925 AN: 5166

South Asian (SAS) AF: 0.348 AC: 1674 AN: 4814

European-Finnish (FIN) AF: 0.486 AC: 5102 AN: 10488

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.582 AC: 39547 AN: 67904

Other (OTH) AF: 0.479 AC: 1005 AN: 2098

Alfa AF: 0.529 Hom.: 80099

Bravo AF: 0.413

Asia WGS AF: 0.284 AC: 987 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.6
DANN	Benign	0.89
PhyloP100		0.065

Splicing

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

Other links and lift over

dbSNP: rs10852344; hg19: chr16-12016919;