rs2903479

Variant names:

• chr3-146234516-A-G
• rs2903479
• NM_020353.3:c.-21-12424T>C

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The NM_020353.3(PLSCR4):​c.-21-12424T>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
• Publications: 0 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=-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 rank	MANE	Protein	UniProt
PLSCR4	NM_020353.3	c.-21-12424T>C		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.-21-12424T>C		intron_variant	Intron 1 of 8	1	NM_020353.3	ENSP00000347038.2

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

African (AFR) AF: 0.699 AC: 28967 AN: 41428

American (AMR) AF: 0.865 AC: 13206 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.891 AC: 3095 AN: 3472

East Asian (EAS) AF: 0.669 AC: 3450 AN: 5158

South Asian (SAS) AF: 0.828 AC: 3993 AN: 4820

European-Finnish (FIN) AF: 0.813 AC: 8605 AN: 10580

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.863 AC: 58666 AN: 68018

Other (OTH) AF: 0.810 AC: 1710 AN: 2110

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
PhyloP100		-0.32
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: rs2903479; hg19: chr3-145952303;