rs11814843

Variant names:

• chr10-69727049-T-C
• rs11814843

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 0.147 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.147 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

African (AFR) AF: 0.330 AC: 13659 AN: 41444

American (AMR) AF: 0.126 AC: 1927 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0643 AC: 223 AN: 3466

East Asian (EAS) AF: 0.0843 AC: 436 AN: 5172

South Asian (SAS) AF: 0.0749 AC: 360 AN: 4808

European-Finnish (FIN) AF: 0.0446 AC: 473 AN: 10608

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.0731 AC: 4973 AN: 67984

Other (OTH) AF: 0.127 AC: 269 AN: 2110

Alfa AF: 0.122 Hom.: 337

Bravo AF: 0.165

Asia WGS AF: 0.0760 AC: 266 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.6
DANN	Benign	0.75
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs11814843; hg19: chr10-71486805;