3-146460314-T-C

Variant names:

• chr3-146460314-T-C
• rs1403641
• ENST00000610787.5:c.-322A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000610787.5. 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	NM_001395437.1	MANE Select	c.-179-231A>G		intron	N/A	NP_001382366.1	Q9NRY7-1
	PLSCR2	NM_001199978.3		c.41-231A>G		intron	N/A	NP_001186907.1	Q9NRY7-2
	PLSCR2	NM_001395440.1		c.41-231A>G		intron	N/A	NP_001382369.1	Q9NRY7-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLSCR2	ENST00000610787.5	TSL:1	c.-322A>G		5_prime_UTR	Exon 1 of 7	ENSP00000478044.1	Q9NRY7-1
	PLSCR2	ENST00000696113.1	MANE Select	c.-179-231A>G		intron	N/A	ENSP00000512407.1	Q9NRY7-1
	PLSCR2	ENST00000613069.4	TSL:1	c.29-231A>G		intron	N/A	ENSP00000478902.1	Q9NRY7-3

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

African (AFR) AF: 0.471 AC: 6551 AN: 13906

American (AMR) AF: 0.682 AC: 5018 AN: 7360

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 5284 AN: 10520

East Asian (EAS) AF: 0.616 AC: 11463 AN: 18608

South Asian (SAS) AF: 0.758 AC: 13552 AN: 17868

European-Finnish (FIN) AF: 0.552 AC: 8436 AN: 15276

Middle Eastern (MID) AF: 0.645 AC: 1247 AN: 1932

European-Non Finnish (NFE) AF: 0.580 AC: 294468 AN: 507330

Other (OTH) AF: 0.586 AC: 16098 AN: 27476

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

African (AFR) AF: 0.478 AC: 19775 AN: 41372

American (AMR) AF: 0.681 AC: 10375 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1811 AN: 3470

East Asian (EAS) AF: 0.628 AC: 3238 AN: 5160

South Asian (SAS) AF: 0.761 AC: 3664 AN: 4814

European-Finnish (FIN) AF: 0.570 AC: 5975 AN: 10490

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.591 AC: 40154 AN: 67908

Other (OTH) AF: 0.573 AC: 1210 AN: 2112

Alfa AF: 0.591 Hom.: 13120

Bravo AF: 0.575

Asia WGS AF: 0.655 AC: 2280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.49
DANN	Benign	0.40
PhyloP100		-0.26
PromoterAI		-0.061	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1403641;

hg19: chr3-146178101;