rs2903479

Positions:

• chr3-146234516-A-G
• chr3-146234516-A-T

Variant summary

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

The NM_020353.3(PLSCR4):​c.-21-12424T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.807 in 152,064 control chromosomes in the GnomAD database, including 49,954 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 0.81 (49954 hom., cov: 32)
• Consequence: PLSCR4 NM_020353.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.315

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]

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 (AMR) allele frequency at 95% confidence interval = 0.857 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLSCR4	NM_020353.3	c.-21-12424T>C		intron_variant		ENST00000354952.7	NP_065086.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLSCR4	ENST00000354952.7	c.-21-12424T>C		intron_variant		1	NM_020353.3	ENSP00000347038	P1

Frequencies

GnomAD3 genomes AF: 0.807 AC: 122636 AN: 151946 Hom.: 49915 Cov.: 32

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.890

Gnomad AMR AF: 0.865

Gnomad ASJ AF: 0.891

Gnomad EAS AF: 0.668

Gnomad SAS AF: 0.829

Gnomad FIN AF: 0.813

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.862

Gnomad OTH AF: 0.811

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

GnomAD4 genome AF: 0.807 AC: 122729 AN: 152064 Hom.: 49954 Cov.: 32 AF XY: 0.805 AC XY: 59805 AN XY: 74320

Gnomad4 AFR AF: 0.699

Gnomad4 AMR AF: 0.865

Gnomad4 ASJ AF: 0.891

Gnomad4 EAS AF: 0.669

Gnomad4 SAS AF: 0.828

Gnomad4 FIN AF: 0.813

Gnomad4 NFE AF: 0.863

Gnomad4 OTH AF: 0.810

Alfa AF: 0.824 Hom.: 3055

Bravo AF: 0.804

Asia WGS AF: 0.725 AC: 2524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.77

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: rs2903479; hg19: chr3-145952303;