rs397266

chr3-138141265-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 0.229 in 151,994 control chromosomes in the GnomAD database, including 4,684 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 0.23 (4684 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.306 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: 0.229 AC: 34813 AN: 151878 Hom.: 4683 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.0527

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.322

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.229 AC: 34819 AN: 151994 Hom.: 4684 Cov.: 32 AF XY: 0.226 AC XY: 16772 AN XY: 74332

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.0532

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.281

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.247

Alfa AF: 0.286 Hom.: 4136

Bravo AF: 0.218

Asia WGS AF: 0.111 AC: 385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	12
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs397266; hg19: chr3-137860107;