rs1354152

Positions:

• chr3-117474331-T-C

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 0.403 in 151,914 control chromosomes in the GnomAD database, including 14,798 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 0.40 (14798 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0630

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61252 AN: 151796 Hom.: 14804 Cov.: 31

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.403 AC: 61226 AN: 151914 Hom.: 14798 Cov.: 31 AF XY: 0.397 AC XY: 29496 AN XY: 74232

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.333

Gnomad4 ASJ AF: 0.517

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.496

Gnomad4 NFE AF: 0.562

Gnomad4 OTH AF: 0.413

Alfa AF: 0.457 Hom.: 3011

Bravo AF: 0.376

Asia WGS AF: 0.327 AC: 1142 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.4
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1354152; hg19: chr3-117193178;