chr3-13881238-C-A

Variant names:

• chr3-13881238-C-A
• rs4685048

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 0.499 in 151,924 control chromosomes in the GnomAD database, including 19,333 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 0.50 (19333 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.724 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: 0.499 AC: 75739 AN: 151808 Hom.: 19324 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.499 AC: 75782 AN: 151924 Hom.: 19333 Cov.: 32 AF XY: 0.503 AC XY: 37349 AN XY: 74248

Gnomad4 AFR AF: 0.422

Gnomad4 AMR AF: 0.552

Gnomad4 ASJ AF: 0.545

Gnomad4 EAS AF: 0.743

Gnomad4 SAS AF: 0.605

Gnomad4 FIN AF: 0.495

Gnomad4 NFE AF: 0.506

Gnomad4 OTH AF: 0.500

Alfa AF: 0.502 Hom.: 29539

Bravo AF: 0.501

Asia WGS AF: 0.632 AC: 2196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.094
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4685048; hg19: chr3-13922735;