3-146234805-T-C

Variant names:

• chr3-146234805-T-C
• rs1877511
• NM_020353.3:c.-21-12713A>G

Variant summary

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

The NM_020353.3(PLSCR4):​c.-21-12713A>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
• 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=-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 rank	MANE	Protein	UniProt
PLSCR4	NM_020353.3	c.-21-12713A>G		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.-21-12713A>G		intron_variant	Intron 1 of 8	1	NM_020353.3	ENSP00000347038.2

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

African (AFR) AF: 0.583 AC: 24149 AN: 41408

American (AMR) AF: 0.852 AC: 13018 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.892 AC: 3094 AN: 3470

East Asian (EAS) AF: 0.668 AC: 3437 AN: 5148

South Asian (SAS) AF: 0.819 AC: 3948 AN: 4820

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

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.862 AC: 58619 AN: 68000

Other (OTH) AF: 0.782 AC: 1651 AN: 2110

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
PhyloP100		0.73
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: rs1877511; hg19: chr3-145952592;