rs4841593

Positions:

• chr8-11768352-G-C
• chr8-11768352-G-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 0.106 in 151,810 control chromosomes in the GnomAD database, including 1,063 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 0.11 (1063 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.431

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.182 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: 0.106 AC: 16042 AN: 151692 Hom.: 1060 Cov.: 31

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0667

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.000774

Gnomad SAS AF: 0.0429

Gnomad FIN AF: 0.0824

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0798

Gnomad OTH AF: 0.0932

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

GnomAD4 genome AF: 0.106 AC: 16061 AN: 151810 Hom.: 1063 Cov.: 31 AF XY: 0.104 AC XY: 7707 AN XY: 74192

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.0665

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.000775

Gnomad4 SAS AF: 0.0433

Gnomad4 FIN AF: 0.0824

Gnomad4 NFE AF: 0.0798

Gnomad4 OTH AF: 0.0917

Alfa AF: 0.0403 Hom.: 33

Bravo AF: 0.108

Asia WGS AF: 0.0320 AC: 112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.0
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4841593; hg19: chr8-11625861;