3-146399254-C-T

Variant names:

• chr3-146399254-C-T
• rs6803636
• ENST00000463633.5:n.101-3333G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000463633.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLSCR2	NR_172559.1		n.652+2106G>A		intron	N/A
	PLSCR2	NR_172561.1		n.1257+2106G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLSCR2	ENST00000463633.5	TSL:3	n.101-3333G>A		intron	N/A	ENSP00000419669.1	F8WEZ1
	ENSG00000241358	ENST00000482888.1	TSL:6	n.295-431G>A		intron	N/A
	ENSG00000293191	ENST00000490344.1	TSL:3	n.343+2106G>A		intron	N/A

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

African (AFR) AF: 0.962 AC: 39966 AN: 41530

American (AMR) AF: 0.876 AC: 13341 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.803 AC: 2782 AN: 3464

East Asian (EAS) AF: 0.729 AC: 3768 AN: 5168

South Asian (SAS) AF: 0.914 AC: 4408 AN: 4824

European-Finnish (FIN) AF: 0.810 AC: 8551 AN: 10560

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.834 AC: 56443 AN: 67692

Other (OTH) AF: 0.844 AC: 1781 AN: 2110

Alfa AF: 0.842 Hom.: 130184

Bravo AF: 0.876

Asia WGS AF: 0.812 AC: 2825 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.52
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs6803636; hg19: chr3-146117041;