22-31619176-C-A

Variant names:

• chr22-31619176-C-A
• rs8461
• ENST00000460723.5:n.1849G>T

Variant summary

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

The ENST00000460723.5(PISD):​n.1849G>T variant causes a non coding transcript exon 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: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PISD ENST00000460723.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150
• Publications: 14 publications found

Genes affected

PISD (HGNC:8999): (phosphatidylserine decarboxylase) The protein encoded by this gene catalyzes the conversion of phosphatidylserine to phosphatidylethanolamine in the inner mitochondrial membrane. The encoded protein is active in phospholipid metabolism and interorganelle trafficking of phosphatidylserine. [provided by RefSeq, May 2016]

PISD Gene-Disease associations (from GenCC):

• Liberfarb syndrome

  Inheritance: AR Classification: STRONG, MODERATE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, Franklin by Genoox, G2P

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=-0.52).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000460723.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PISD	NM_001326411.2	MANE Select	c.*436G>T		3_prime_UTR	Exon 8 of 8	NP_001313340.1
	PISD	NM_001326412.1		c.*436G>T		3_prime_UTR	Exon 8 of 8	NP_001313341.1
	PISD	NM_001326413.2		c.*436G>T		3_prime_UTR	Exon 8 of 8	NP_001313342.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PISD	ENST00000460723.5	TSL:1	n.1849G>T		non_coding_transcript_exon	Exon 7 of 7
	PISD	ENST00000439502.7	TSL:1 MANE Select	c.*436G>T		3_prime_UTR	Exon 8 of 8	ENSP00000391739.2
	PISD	ENST00000266095.9	TSL:1	c.*436G>T		3_prime_UTR	Exon 9 of 9	ENSP00000266095.5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 126128 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 68770

African (AFR) AF: 0.00 AC: 0 AN: 2974

American (AMR) AF: 0.00 AC: 0 AN: 4868

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2782

East Asian (EAS) AF: 0.00 AC: 0 AN: 4446

South Asian (SAS) AF: 0.00 AC: 0 AN: 25486

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6280

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 438

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 72832

Other (OTH) AF: 0.00 AC: 0 AN: 6022

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 8023

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	8.8
DANN	Benign	0.84
PhyloP100		0.015

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: rs8461; hg19: chr22-32015162;