rs1394041

Positions:

• chr3-147379060-C-A

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/exons	MANE	UniProt

Ensembl

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