3-146234805-T-C

Position:

• chr3-146234805-T-C

Variant summary

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

The NM_020353.3(PLSCR4):​c.-21-12713A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.773 in 152,016 control chromosomes in the GnomAD database, including 46,609 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 0.77 (46609 hom., cov: 31)
• Consequence: PLSCR4 NM_020353.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.726

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.856 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLSCR4	NM_020353.3	c.-21-12713A>G		intron_variant		ENST00000354952.7	NP_065086.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLSCR4	ENST00000354952.7	c.-21-12713A>G		intron_variant		1	NM_020353.3	ENSP00000347038	P1

Frequencies

GnomAD3 genomes AF: 0.774 AC: 117494 AN: 151898 Hom.: 46583 Cov.: 31

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.890

Gnomad AMR AF: 0.852

Gnomad ASJ AF: 0.892

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.819

Gnomad FIN AF: 0.813

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.862

Gnomad OTH AF: 0.789

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

GnomAD4 genome AF: 0.773 AC: 117557 AN: 152016 Hom.: 46609 Cov.: 31 AF XY: 0.771 AC XY: 57329 AN XY: 74310

Gnomad4 AFR AF: 0.583

Gnomad4 AMR AF: 0.852

Gnomad4 ASJ AF: 0.892

Gnomad4 EAS AF: 0.668

Gnomad4 SAS AF: 0.819

Gnomad4 FIN AF: 0.813

Gnomad4 NFE AF: 0.862

Gnomad4 OTH AF: 0.782

Alfa AF: 0.820 Hom.: 6437

Bravo AF: 0.766

Asia WGS AF: 0.703 AC: 2449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.5
DANN	Benign	0.80

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: rs1877511; hg19: chr3-145952592;