rs780823329

Variant names:

• chr8-22927603-C-G
• NM_144962.3:c.112G>C

Your query was ambiguous. Multiple possible variants found:

• chr8-22927603-C-G
• chr8-22927603-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_144962.3(PEBP4):​c.112G>C​(p.Glu38Gln) variant causes a missense 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. 14/21 in silico tools predict 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: 33)
• Consequence: PEBP4 NM_144962.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950

Genes affected

PEBP4 (HGNC:28319): (phosphatidylethanolamine binding protein 4) The phosphatidylethanolamine (PE)-binding proteins, including PEBP4, are an evolutionarily conserved family of proteins with pivotal biologic functions, such as lipid binding and inhibition of serine proteases (Wang et al., 2004 [PubMed 15302887]).[supplied by OMIM, Dec 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.114751816).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PEBP4	NM_144962.3	c.112G>C	p.Glu38Gln	missense_variant	Exon 2 of 7	ENST00000256404.8	NP_659399.2
PEBP4	NM_001363233.2	c.112G>C	p.Glu38Gln	missense_variant	Exon 2 of 7		NP_001350162.1
PEBP4	XM_017013103.2	c.112G>C	p.Glu38Gln	missense_variant	Exon 2 of 3		XP_016868592.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PEBP4	ENST00000256404.8	c.112G>C	p.Glu38Gln	missense_variant	Exon 2 of 7	1	NM_144962.3	ENSP00000256404.6
PEBP4	ENST00000522278.1	c.262G>C	p.Glu88Gln	missense_variant	Exon 2 of 2	5		ENSP00000429414.1
PEBP4	ENST00000521284.1	n.183G>C		non_coding_transcript_exon_variant	Exon 2 of 5	3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.098
BayesDel_addAF	Benign	-0.28	T
BayesDel_noAF	Benign	-0.64
CADD	Benign	2.3
DANN	Benign	0.82
DEOGEN2	Benign	0.0049	T;.
Eigen	Benign	-0.91
Eigen_PC	Benign	-0.94
FATHMM_MKL	Benign	0.064	N
LIST_S2	Benign	0.35	T;T
M_CAP	Benign	0.0043	T
MetaRNN	Benign	0.11	T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.5	L;.
PrimateAI	Benign	0.23	T
PROVEAN	Benign	-0.35	N;D
REVEL	Benign	0.046
Sift	Benign	0.22	T;T
Sift4G	Benign	0.54	T;.
Polyphen		0.082	B;.
Vest4		0.13
MutPred		0.50		Gain of sheet (P = 0.0344);.;
MVP		0.15
MPC		0.017
ClinPred		0.17	T
GERP RS		2.2
Varity_R		0.054
gMVP		0.51

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr8-22785116;