3-146460314-T-C

Position:

• chr3-146460314-T-C

Variant summary

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

The ENST00000610787.5(PLSCR2):​c.-322A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.582 in 772,048 control chromosomes in the GnomAD database, including 132,469 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 0.57 (25417 hom., cov: 30)
  • Exomes 𝑓: 0.58 (107052 hom.)
• Consequence: PLSCR2 ENST00000610787.5 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.259

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLSCR2	NM_001395437.1	c.-179-231A>G		intron_variant		ENST00000696113.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLSCR2	ENST00000696113.1	c.-179-231A>G		intron_variant			NM_001395437.1	P1

Frequencies

GnomAD3 genomes AF: 0.573 AC: 86916 AN: 151654 Hom.: 25388 Cov.: 30

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.680

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.573

GnomAD4 exome AF: 0.584 AC: 362117 AN: 620276 Hom.: 107052 Cov.: 9 AF XY: 0.587 AC XY: 177048 AN XY: 301688

Gnomad4 AFR exome AF: 0.471

Gnomad4 AMR exome AF: 0.682

Gnomad4 ASJ exome AF: 0.502

Gnomad4 EAS exome AF: 0.616

Gnomad4 SAS exome AF: 0.758

Gnomad4 FIN exome AF: 0.552

Gnomad4 NFE exome AF: 0.580

Gnomad4 OTH exome AF: 0.586

GnomAD4 genome AF: 0.573 AC: 86994 AN: 151772 Hom.: 25417 Cov.: 30 AF XY: 0.579 AC XY: 42937 AN XY: 74166

Gnomad4 AFR AF: 0.478

Gnomad4 AMR AF: 0.681

Gnomad4 ASJ AF: 0.522

Gnomad4 EAS AF: 0.628

Gnomad4 SAS AF: 0.761

Gnomad4 FIN AF: 0.570

Gnomad4 NFE AF: 0.591

Gnomad4 OTH AF: 0.573

Alfa AF: 0.594 Hom.: 11739

Bravo AF: 0.575

Asia WGS AF: 0.655 AC: 2280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.49
DANN	Benign	0.40

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1403641; hg19: chr3-146178101;