rs4755392

chr11-35232539-T-Achr11-35232539-T-C

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 0.424 in 151,872 control chromosomes in the GnomAD database, including 13,999 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 0.42 (13999 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.467

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.544 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: 0.424 AC: 64352 AN: 151754 Hom.: 14005 Cov.: 31

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.424 AC: 64363 AN: 151872 Hom.: 13999 Cov.: 31 AF XY: 0.430 AC XY: 31925 AN XY: 74218

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.555

Gnomad4 EAS AF: 0.458

Gnomad4 SAS AF: 0.561

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.461

Gnomad4 OTH AF: 0.425

Alfa AF: 0.300 Hom.: 795

Bravo AF: 0.407

Asia WGS AF: 0.463 AC: 1607 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	0.49
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4755392; hg19: chr11-35254086;