11-50137254-C-T

Variant names:

• chr11-50137254-C-T
• rs4881702

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 0.137 in 152,062 control chromosomes in the GnomAD database, including 1,851 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 0.14 (1851 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.696
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.234 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: 0.136 AC: 20733 AN: 151942 Hom.: 1845 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.0688

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.0493

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0851

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.137 AC: 20771 AN: 152062 Hom.: 1851 Cov.: 32 AF XY: 0.137 AC XY: 10181 AN XY: 74336

African (AFR) AF: 0.233 AC: 9656 AN: 41446

American (AMR) AF: 0.121 AC: 1842 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0688 AC: 239 AN: 3472

East Asian (EAS) AF: 0.245 AC: 1266 AN: 5164

South Asian (SAS) AF: 0.235 AC: 1135 AN: 4822

European-Finnish (FIN) AF: 0.0493 AC: 522 AN: 10598

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0851 AC: 5785 AN: 67980

Other (OTH) AF: 0.122 AC: 258 AN: 2110

Alfa AF: 0.0886 Hom.: 422

Bravo AF: 0.143

Asia WGS AF: 0.272 AC: 944 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.4
DANN	Benign	0.41
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs4881702; hg19: chr11-50096425;