rs1394041

Variant names:

• chr3-147379060-C-A
• rs1394041

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0962 in 152,132 control chromosomes in the GnomAD database, including 843 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 0.096 (843 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.33

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.154 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: 0.0963 AC: 14636 AN: 152014 Hom.: 844 Cov.: 33

Gnomad AFR AF: 0.0323

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0853

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.0863

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

GnomAD4 genome AF: 0.0962 AC: 14641 AN: 152132 Hom.: 843 Cov.: 33 AF XY: 0.0984 AC XY: 7319 AN XY: 74350

Gnomad4 AFR AF: 0.0322

Gnomad4 AMR AF: 0.0852

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.174

Gnomad4 NFE AF: 0.119

Gnomad4 OTH AF: 0.0868

Alfa AF: 0.111 Hom.: 1337

Bravo AF: 0.0869

Asia WGS AF: 0.132 AC: 461 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
CADD	Benign	22
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1394041; hg19: chr3-147096847;