rs9942773

chr8-114108798-A-Cchr8-114108798-A-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 0.247 in 151,848 control chromosomes in the GnomAD database, including 4,925 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 0.25 (4925 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.587

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 = 0.299 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: 0.247 AC: 37534 AN: 151730 Hom.: 4919 Cov.: 31

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.0425

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.247 AC: 37560 AN: 151848 Hom.: 4925 Cov.: 31 AF XY: 0.241 AC XY: 17908 AN XY: 74172

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.0428

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.229

Gnomad4 NFE AF: 0.258

Gnomad4 OTH AF: 0.226

Alfa AF: 0.141 Hom.: 267

Bravo AF: 0.246

Asia WGS AF: 0.116 AC: 408 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	2.1
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9942773; hg19: chr8-115121027;