rs4352381

Variant names:

• chr3-163978652-C-G
• rs4352381

Your query was ambiguous. Multiple possible variants found:

• chr3-163978652-C-G
• chr3-163978652-C-T

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 0.296 in 151,918 control chromosomes in the GnomAD database, including 7,384 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 0.30 (7384 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600
• 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 (EAS) allele frequency at 95% confidence interval = 0.558 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: 0.296 AC: 44930 AN: 151800 Hom.: 7373 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.296 AC: 44960 AN: 151918 Hom.: 7384 Cov.: 32 AF XY: 0.299 AC XY: 22231 AN XY: 74236

African (AFR) AF: 0.184 AC: 7624 AN: 41482

American (AMR) AF: 0.365 AC: 5561 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 1379 AN: 3472

East Asian (EAS) AF: 0.575 AC: 2966 AN: 5154

South Asian (SAS) AF: 0.367 AC: 1771 AN: 4824

European-Finnish (FIN) AF: 0.285 AC: 3012 AN: 10558

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.313 AC: 21270 AN: 67898

Other (OTH) AF: 0.346 AC: 730 AN: 2108

Alfa AF: 0.297 Hom.: 849

Bravo AF: 0.299

Asia WGS AF: 0.477 AC: 1658 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.6
DANN	Benign	0.66
PhyloP100		-0.0060

Splicing

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

Other links and lift over

dbSNP: rs4352381; hg19: chr3-163696440;