11-118847776-C-T

Variant names:

• chr11-118847776-C-T
• rs4938561

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 0.794 in 152,024 control chromosomes in the GnomAD database, including 48,240 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 0.79 (48240 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.670

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.87 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: 0.794 AC: 120636 AN: 151904 Hom.: 48176 Cov.: 30

Gnomad AFR AF: 0.877

Gnomad AMI AF: 0.794

Gnomad AMR AF: 0.852

Gnomad ASJ AF: 0.815

Gnomad EAS AF: 0.726

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.764

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.794 AC: 120759 AN: 152024 Hom.: 48240 Cov.: 30 AF XY: 0.790 AC XY: 58713 AN XY: 74288

Gnomad4 AFR AF: 0.877

Gnomad4 AMR AF: 0.853

Gnomad4 ASJ AF: 0.815

Gnomad4 EAS AF: 0.726

Gnomad4 SAS AF: 0.609

Gnomad4 FIN AF: 0.723

Gnomad4 NFE AF: 0.759

Gnomad4 OTH AF: 0.797

Alfa AF: 0.761 Hom.: 55346

Bravo AF: 0.811

Asia WGS AF: 0.685 AC: 2385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4938561; hg19: chr11-118718485;