rs9838168

chr3-137245125-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 0.348 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.469

Gnomad4 EAS AF: 0.386

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.370

Gnomad4 NFE AF: 0.470

Gnomad4 OTH AF: 0.402

Alfa AF: 0.451 Hom.: 32097

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9838168; hg19: chr3-136963967;