11-118871133-C-T

Variant names:

• chr11-118871133-C-T
• rs4938573

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 0.792 in 150,166 control chromosomes in the GnomAD database, including 46,966 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 (46966 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.858 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: 0.792 AC: 118800 AN: 150054 Hom.: 46939 Cov.: 25

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.826

Gnomad ASJ AF: 0.827

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.854

Gnomad FIN AF: 0.843

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.813

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

GnomAD4 genome AF: 0.792 AC: 118879 AN: 150166 Hom.: 46966 Cov.: 25 AF XY: 0.796 AC XY: 58258 AN XY: 73224

Gnomad4 AFR AF: 0.725

Gnomad4 AMR AF: 0.826

Gnomad4 ASJ AF: 0.827

Gnomad4 EAS AF: 0.879

Gnomad4 SAS AF: 0.853

Gnomad4 FIN AF: 0.843

Gnomad4 NFE AF: 0.803

Gnomad4 OTH AF: 0.815

Alfa AF: 0.804 Hom.: 99360

Bravo AF: 0.786

Asia WGS AF: 0.852 AC: 2963 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.0020
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4938573; hg19: chr11-118741842;