11-13150176-C-T

Variant names:

• chr11-13150176-C-T
• rs1441351

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4 BA1

The variant allele was found at a frequency of 0.118 in 152,010 control chromosomes in the GnomAD database, including 3,268 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 0.12 (3268 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.543

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.12).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.386 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: 0.118 AC: 17897 AN: 151892 Hom.: 3250 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0671

Gnomad ASJ AF: 0.0159

Gnomad EAS AF: 0.0598

Gnomad SAS AF: 0.00725

Gnomad FIN AF: 0.0000943

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00238

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.118 AC: 17963 AN: 152010 Hom.: 3268 Cov.: 32 AF XY: 0.114 AC XY: 8506 AN XY: 74336

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.0674

Gnomad4 ASJ AF: 0.0159

Gnomad4 EAS AF: 0.0595

Gnomad4 SAS AF: 0.00705

Gnomad4 FIN AF: 0.0000943

Gnomad4 NFE AF: 0.00237

Gnomad4 OTH AF: 0.0997

Alfa AF: 0.0165 Hom.: 220

Bravo AF: 0.138

Asia WGS AF: 0.0730 AC: 253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.12
CADD	Benign	15
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1441351; hg19: chr11-13171723;