3-146399254-C-T

Position:

• chr3-146399254-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000463633.5(PLSCR2):​n.101-3333G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.87 in 151,788 control chromosomes in the GnomAD database, including 57,790 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 0.87 (57790 hom., cov: 32)
• Consequence: PLSCR2 ENST00000463633.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.391

Genes affected

PLSCR2 (HGNC:16494): (phospholipid scramblase 2) This gene encodes a member of the phospholipid scramblase family. Phospholipid scramblases are membrane proteins that mediate calcium-dependent, non-specific movement of plasma membrane phospholipids and phosphatidylserine exposure. The encoded protein contains a low affinity calcium binding motif and may play a role in blood coagulation and apoptosis. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jan 2011]

ENSG00000241358 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.954 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLSCR2	NR_172559.1	n.652+2106G>A		intron_variant
PLSCR2	NR_172561.1	n.1257+2106G>A		intron_variant
PLSCR2	XR_002959557.2	n.3868+2106G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLSCR2	ENST00000463633.5	n.101-3333G>A		intron_variant		3		ENSP00000419669.1
ENSG00000241358	ENST00000482888.1	n.295-431G>A		intron_variant		6
ENSG00000241358	ENST00000490344.1	n.343+2106G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.870 AC: 131968 AN: 151670 Hom.: 57727 Cov.: 32

Gnomad AFR AF: 0.962

Gnomad AMI AF: 0.862

Gnomad AMR AF: 0.875

Gnomad ASJ AF: 0.803

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.914

Gnomad FIN AF: 0.810

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.834

Gnomad OTH AF: 0.848

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

GnomAD4 genome AF: 0.870 AC: 132089 AN: 151788 Hom.: 57790 Cov.: 32 AF XY: 0.869 AC XY: 64493 AN XY: 74186

Gnomad4 AFR AF: 0.962

Gnomad4 AMR AF: 0.876

Gnomad4 ASJ AF: 0.803

Gnomad4 EAS AF: 0.729

Gnomad4 SAS AF: 0.914

Gnomad4 FIN AF: 0.810

Gnomad4 NFE AF: 0.834

Gnomad4 OTH AF: 0.844

Alfa AF: 0.837 Hom.: 97342

Bravo AF: 0.876

Asia WGS AF: 0.812 AC: 2825 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6803636; hg19: chr3-146117041;