rs4685048

chr3-13881238-C-Achr3-13881238-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 0.499 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;