3-146233543-C-T

Variant names:

• chr3-146233543-C-T
• rs1512890
• NM_020353.3:c.-21-11451G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020353.3(PLSCR4):​c.-21-11451G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.71 in 151,970 control chromosomes in the GnomAD database, including 40,891 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 0.71 (40891 hom., cov: 32)
• Consequence: PLSCR4 NM_020353.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 1 publications found

Genes affected

PLSCR4 (HGNC:16497): (phospholipid scramblase 4) Enables CD4 receptor binding activity and enzyme binding activity. Predicted to be involved in plasma membrane phospholipid scrambling. Predicted to act upstream of or within cellular response to lipopolysaccharide. Located in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000297339 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.841 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLSCR4	NM_020353.3	c.-21-11451G>A		intron_variant	Intron 1 of 8	ENST00000354952.7	NP_065086.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLSCR4	ENST00000354952.7	c.-21-11451G>A		intron_variant	Intron 1 of 8	1	NM_020353.3	ENSP00000347038.2

Frequencies

GnomAD3 genomes AF: 0.711 AC: 107933 AN: 151852 Hom.: 40894 Cov.: 32

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.873

Gnomad AMR AF: 0.751

Gnomad ASJ AF: 0.886

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.795

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.847

Gnomad OTH AF: 0.737

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

GnomAD4 genome AF: 0.710 AC: 107952 AN: 151970 Hom.: 40891 Cov.: 32 AF XY: 0.709 AC XY: 52674 AN XY: 74270

African (AFR) AF: 0.424 AC: 17553 AN: 41428

American (AMR) AF: 0.751 AC: 11458 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.886 AC: 3075 AN: 3470

East Asian (EAS) AF: 0.667 AC: 3451 AN: 5174

South Asian (SAS) AF: 0.795 AC: 3822 AN: 4806

European-Finnish (FIN) AF: 0.805 AC: 8515 AN: 10578

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.847 AC: 57519 AN: 67940

Other (OTH) AF: 0.731 AC: 1546 AN: 2114

Alfa AF: 0.791 Hom.: 101612

Bravo AF: 0.690

Asia WGS AF: 0.672 AC: 2336 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.25
DANN	Benign	0.32
PhyloP100		-1.3
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

Other links and lift over

dbSNP: rs1512890; hg19: chr3-145951330;