Variant rs4613118 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_020360.4(PLSCR3):c.-23T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.799 in 1,610,976 control chromosomes in the GnomAD database, including 530,043 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 0.70 ( 39774 hom., cov: 30)

Exomes 𝑓: 0.81 ( 490269 hom. )

Consequence

PLSCR3
NM_020360.4 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.18

Variant links:

Genes affected

PLSCR3 (HGNC:16495): (phospholipid scramblase 3) Enables several functions, including calcium-dependent protein binding activity; metal ion binding activity; and phospholipid scramblase activity. Involved in several processes, including cardiolipin biosynthetic process; regulation of apoptotic process; and regulation of release of cytochrome c from mitochondria. Located in cytosol; mitochondrion; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

PLSCR3 links:

TMEM256-PLSCR3 (HGNC:49186): (TMEM256-PLSCR3 readthrough (NMD candidate)) This locus represents naturally occurring read-through transcription between the neighboring chromosome 17 open reading frame 61 (C17orf61) and phospholipid scramblase 3 (PLSCR3) genes. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is unlikely to produce a protein product. [provided by RefSeq, Jan 2011]

TMEM256-PLSCR3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 = 0.847 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLSCR3	NM_020360.4 link	c.-23T>C		5_prime_UTR_variant	2/8	ENST00000619711.5	NP_065093.2	Q9NRY6

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
PLSCR3	ENST00000619711.5 link	c.-23T>C	5_prime_UTR_variant	2/8	5	NM_020360.4	ENSP00000483743.2	Q9NRY6
TMEM256-PLSCR3	ENST00000573331.5 link	n.*776T>C	non_coding_transcript_exon_variant	5/11	2		ENSP00000466104.1	K7ERE1
TMEM256-PLSCR3	ENST00000573331.5 link	n.*776T>C	3_prime_UTR_variant	5/11	2		ENSP00000466104.1	K7ERE1

Frequencies

GnomAD3 genomes

AF:

0.702

AC:

106546

AN:

151768

Hom.:

39770

Cov.:

show subpopulations

Gnomad AFR

AF:

0.506

Gnomad AMI

AF:

0.913

Gnomad AMR

AF:

0.577

Gnomad ASJ

AF:

0.798

Gnomad EAS

AF:

0.301

Gnomad SAS

AF:

0.675

Gnomad FIN

AF:

0.826

Gnomad MID

AF:

0.788

Gnomad NFE

AF:

0.853

Gnomad OTH

AF:

0.724

GnomAD3 exomes

AF:

0.707

AC:

173903

AN:

245826

Hom.:

66605

AF XY:

0.726

AC XY:

97056

AN XY:

133666

show subpopulations

Gnomad AFR exome

AF:

0.497

Gnomad AMR exome

AF:

0.425

Gnomad ASJ exome

AF:

0.811

Gnomad EAS exome

AF:

0.300

Gnomad SAS exome

AF:

0.711

Gnomad FIN exome

AF:

0.832

Gnomad NFE exome

AF:

0.854

Gnomad OTH exome

AF:

0.756

GnomAD4 exome

AF:

0.809

AC:

1179949

AN:

1459090

Hom.:

490269

Cov.:

AF XY:

0.809

AC XY:

587073

AN XY:

725882

show subpopulations

Gnomad4 AFR exome

AF:

0.503

Gnomad4 AMR exome

AF:

0.442

Gnomad4 ASJ exome

AF:

0.812

Gnomad4 EAS exome

AF:

0.291

Gnomad4 SAS exome

AF:

0.707

Gnomad4 FIN exome

AF:

0.839

Gnomad4 NFE exome

AF:

0.859

Gnomad4 OTH exome

AF:

0.779

GnomAD4 genome

AF:

0.702

AC:

106597

AN:

151886

Hom.:

39774

Cov.:

AF XY:

0.694

AC XY:

51505

AN XY:

74238

show subpopulations

Gnomad4 AFR

AF:

0.506

Gnomad4 AMR

AF:

0.576

Gnomad4 ASJ

AF:

0.798

Gnomad4 EAS

AF:

0.300

Gnomad4 SAS

AF:

0.677

Gnomad4 FIN

AF:

0.826

Gnomad4 NFE

AF:

0.853

Gnomad4 OTH

AF:

0.718

Alfa

AF:

0.816

Hom.:

49451

Bravo

AF:

0.669

Asia WGS

AF:

0.487

AC:

1695

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

DANN

Benign

0.50

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over