rs9838168

Variant names:

• chr3-137245125-C-T
• rs9838168

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.348 in 151,912 control chromosomes in the GnomAD database, including 11,292 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 0.35 (11292 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.466 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: 0.348 AC: 52879 AN: 151794 Hom.: 11287 Cov.: 31

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.348 AC: 52884 AN: 151912 Hom.: 11292 Cov.: 31 AF XY: 0.345 AC XY: 25595 AN XY: 74226

African (AFR) AF: 0.103 AC: 4267 AN: 41464

American (AMR) AF: 0.431 AC: 6582 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1625 AN: 3466

East Asian (EAS) AF: 0.386 AC: 1984 AN: 5146

South Asian (SAS) AF: 0.220 AC: 1060 AN: 4812

European-Finnish (FIN) AF: 0.370 AC: 3904 AN: 10540

Middle Eastern (MID) AF: 0.438 AC: 128 AN: 292

European-Non Finnish (NFE) AF: 0.470 AC: 31945 AN: 67928

Other (OTH) AF: 0.402 AC: 845 AN: 2100

Alfa AF: 0.428 Hom.: 46017

Bravo AF: 0.344

Asia WGS AF: 0.297 AC: 1032 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.82
DANN	Benign	0.93
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs9838168; hg19: chr3-136963967;