11-123886178-C-G

Variant names:

• chr11-123886178-C-G
• rs7941883

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 0.626 in 151,426 control chromosomes in the GnomAD database, including 30,372 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 0.63 (30372 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.22
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.758 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: 0.626 AC: 94747 AN: 151314 Hom.: 30318 Cov.: 28

Gnomad AFR AF: 0.765

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.606

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

GnomAD4 genome AF: 0.626 AC: 94856 AN: 151426 Hom.: 30372 Cov.: 28 AF XY: 0.626 AC XY: 46312 AN XY: 73960

African (AFR) AF: 0.765 AC: 31580 AN: 41282

American (AMR) AF: 0.648 AC: 9854 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.640 AC: 2218 AN: 3468

East Asian (EAS) AF: 0.572 AC: 2916 AN: 5102

South Asian (SAS) AF: 0.542 AC: 2584 AN: 4770

European-Finnish (FIN) AF: 0.572 AC: 5989 AN: 10474

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.556 AC: 37730 AN: 67822

Other (OTH) AF: 0.601 AC: 1264 AN: 2104

Alfa AF: 0.583 Hom.: 3160

Bravo AF: 0.640

Asia WGS AF: 0.554 AC: 1926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.020
DANN	Benign	0.59
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs7941883; hg19: chr11-123756885;