rs11167023

Positions:

• chr8-141096129-G-A
• chr8-141096129-G-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 0.245 in 151,888 control chromosomes in the GnomAD database, including 5,056 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 0.25 (5056 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0690

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37265 AN: 151774 Hom.: 5048 Cov.: 32

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.0703

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.245 AC: 37286 AN: 151888 Hom.: 5056 Cov.: 32 AF XY: 0.249 AC XY: 18473 AN XY: 74240

Gnomad4 AFR AF: 0.328

Gnomad4 AMR AF: 0.273

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.389

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.213

Alfa AF: 0.195 Hom.: 6634

Bravo AF: 0.247

Asia WGS AF: 0.348 AC: 1209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.6
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11167023; hg19: chr8-142106228;