rs11814843

Positions:

• chr10-69727049-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;