rs4252243

Positions:

• chr11-117985012-C-T

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 0.162 in 151,860 control chromosomes in the GnomAD database, including 2,362 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 0.16 (2362 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.09).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24545 AN: 151742 Hom.: 2350 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.0923

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.0946

Gnomad EAS AF: 0.0734

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.162 AC: 24597 AN: 151860 Hom.: 2362 Cov.: 32 AF XY: 0.161 AC XY: 11935 AN XY: 74222

Gnomad4 AFR AF: 0.271

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.0946

Gnomad4 EAS AF: 0.0731

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.155

Alfa AF: 0.119 Hom.: 1206

Bravo AF: 0.172

Asia WGS AF: 0.151 AC: 525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	2.2
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4252243; hg19: chr11-117855727;