rs10892353

Variant names:

• chr11-119350739-G-A
• rs10892353

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 0.184 in 152,212 control chromosomes in the GnomAD database, including 2,980 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 0.18 (2980 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.184 AC: 28011 AN: 152094 Hom.: 2968 Cov.: 31

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.184 AC: 28058 AN: 152212 Hom.: 2980 Cov.: 31 AF XY: 0.189 AC XY: 14030 AN XY: 74418

African (AFR) AF: 0.203 AC: 8411 AN: 41516

American (AMR) AF: 0.242 AC: 3706 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 611 AN: 3468

East Asian (EAS) AF: 0.346 AC: 1794 AN: 5188

South Asian (SAS) AF: 0.397 AC: 1912 AN: 4818

European-Finnish (FIN) AF: 0.108 AC: 1144 AN: 10610

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.145 AC: 9890 AN: 68000

Other (OTH) AF: 0.198 AC: 419 AN: 2112

Alfa AF: 0.179 Hom.: 3735

Bravo AF: 0.196

Asia WGS AF: 0.396 AC: 1373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.62
PhyloP100		0.026

Splicing

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

Other links and lift over

dbSNP: rs10892353; hg19: chr11-119221449;