rs231146

Positions:

• chr8-115404761-C-G
• chr8-115404761-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 0.515 in 151,850 control chromosomes in the GnomAD database, including 20,457 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 0.52 (20457 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.701

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.587 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: 0.515 AC: 78161 AN: 151732 Hom.: 20412 Cov.: 31

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.515 AC: 78268 AN: 151850 Hom.: 20457 Cov.: 31 AF XY: 0.511 AC XY: 37923 AN XY: 74216

Gnomad4 AFR AF: 0.593

Gnomad4 AMR AF: 0.475

Gnomad4 ASJ AF: 0.396

Gnomad4 EAS AF: 0.529

Gnomad4 SAS AF: 0.554

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.475

Alfa AF: 0.508 Hom.: 2436

Bravo AF: 0.525

Asia WGS AF: 0.536 AC: 1864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.59
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs231146; hg19: chr8-116416989;