rs1403641

Variant names:

• chr3-146460314-T-A
• rs1403641
• ENST00000610787.5:c.-322A>T

Your query was ambiguous. Multiple possible variants found:

• chr3-146460314-T-A
• chr3-146460314-T-C
• chr3-146460314-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000610787.5(PLSCR2):​c.-322A>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PLSCR2 ENST00000610787.5 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.259
• Publications: 5 publications found

Genes affected

PLSCR2 (HGNC:16494): (phospholipid scramblase 2) This gene encodes a member of the phospholipid scramblase family. Phospholipid scramblases are membrane proteins that mediate calcium-dependent, non-specific movement of plasma membrane phospholipids and phosphatidylserine exposure. The encoded protein contains a low affinity calcium binding motif and may play a role in blood coagulation and apoptosis. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jan 2011]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000610787.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLSCR2	NM_001395437.1	MANE Select	c.-179-231A>T		intron	N/A	NP_001382366.1	Q9NRY7-1
	PLSCR2	NM_001199978.3		c.41-231A>T		intron	N/A	NP_001186907.1	Q9NRY7-2
	PLSCR2	NM_001395440.1		c.41-231A>T		intron	N/A	NP_001382369.1	Q9NRY7-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLSCR2	ENST00000610787.5	TSL:1	c.-322A>T		5_prime_UTR_premature_start_codon_gain	Exon 1 of 7	ENSP00000478044.1	Q9NRY7-1
	PLSCR2	ENST00000610787.5	TSL:1	c.-322A>T		5_prime_UTR	Exon 1 of 7	ENSP00000478044.1	Q9NRY7-1
	PLSCR2	ENST00000696113.1	MANE Select	c.-179-231A>T		intron	N/A	ENSP00000512407.1	Q9NRY7-1

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 623166 Hom.: 0 Cov.: 9 AF XY: 0.00 AC XY: 0 AN XY: 303110

African (AFR) AF: 0.00 AC: 0 AN: 13966

American (AMR) AF: 0.00 AC: 0 AN: 7386

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 10576

East Asian (EAS) AF: 0.00 AC: 0 AN: 18708

South Asian (SAS) AF: 0.00 AC: 0 AN: 17916

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 15370

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1936

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 509724

Other (OTH) AF: 0.00 AC: 0 AN: 27584

GnomAD4 genome Cov.: 30

Alfa AF: 0.00 Hom.: 13120

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.41
DANN	Benign	0.42
PhyloP100		-0.26
PromoterAI		-0.018	Neutral

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1403641;

hg19: chr3-146178101;