rs11812365

Variant names:

• chr10-49261236-T-C
• rs11812365

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 0.176 in 148,652 control chromosomes in the GnomAD database, including 2,651 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 (2651 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.279 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: 0.176 AC: 26190 AN: 148544 Hom.: 2648 Cov.: 31

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.106

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.176 AC: 26204 AN: 148652 Hom.: 2651 Cov.: 31 AF XY: 0.177 AC XY: 12798 AN XY: 72220

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.185

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.170

Alfa AF: 0.142 Hom.: 1441

Bravo AF: 0.174

Asia WGS AF: 0.159 AC: 551 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.9
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11812365; hg19: chr10-50469281;