11-123886178-C-G

Position:

• chr11-123886178-C-G

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 0.626 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.765

Gnomad4 AMR AF: 0.648

Gnomad4 ASJ AF: 0.640

Gnomad4 EAS AF: 0.572

Gnomad4 SAS AF: 0.542

Gnomad4 FIN AF: 0.572

Gnomad4 NFE AF: 0.556

Gnomad4 OTH AF: 0.601

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7941883; hg19: chr11-123756885;