rs11814843

Variant names:

• chr10-69727049-T-C
• rs11814843

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 0.147 in 152,072 control chromosomes in the GnomAD database, including 2,695 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 0.15 (2695 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.325 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: 0.147 AC: 22374 AN: 151954 Hom.: 2689 Cov.: 32

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.0505

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.0643

Gnomad EAS AF: 0.0841

Gnomad SAS AF: 0.0748

Gnomad FIN AF: 0.0446

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0732

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.147 AC: 22409 AN: 152072 Hom.: 2695 Cov.: 32 AF XY: 0.143 AC XY: 10610 AN XY: 74332

Gnomad4 AFR AF: 0.330

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.0643

Gnomad4 EAS AF: 0.0843

Gnomad4 SAS AF: 0.0749

Gnomad4 FIN AF: 0.0446

Gnomad4 NFE AF: 0.0731

Gnomad4 OTH AF: 0.127

Alfa AF: 0.116 Hom.: 297

Bravo AF: 0.165

Asia WGS AF: 0.0760 AC: 266 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.6
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: rs11814843; hg19: chr10-71486805;