rs4252243

Variant names:

• chr11-117985012-C-T
• rs4252243

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;