rs10892353

Variant names:

• chr11-119350739-G-A
• rs10892353

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 0.184 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.184 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

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.346

Gnomad4 SAS AF: 0.397

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.145

Gnomad4 OTH AF: 0.198

Alfa AF: 0.171 Hom.: 2072

Bravo AF: 0.196

Asia WGS AF: 0.396 AC: 1373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
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: rs10892353; hg19: chr11-119221449;