ENST00000442122.5:n.*440+1981G>A

Variant names:

• chr2-216037210-C-T
• rs934154
• ENST00000442122.5:n.*440+1981G>A

Variant summary

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

The ENST00000442122.5(PECR):​n.*440+1981G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.723 in 152,186 control chromosomes in the GnomAD database, including 39,983 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 0.72 (39983 hom., cov: 33)
• Consequence: PECR ENST00000442122.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.936
• Publications: 2 publications found

Genes affected

PECR (HGNC:18281): (peroxisomal trans-2-enoyl-CoA reductase) Enables signaling receptor binding activity and trans-2-enoyl-CoA reductase (NADPH) activity. Involved in phytol metabolic process. Located in peroxisome. [provided by Alliance of Genome Resources, Apr 2022]

PECR Gene-Disease associations (from GenCC):

• neurodevelopmental disorder

  Inheritance: AR Classification: LIMITED Submitted by: G2P

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PECR	XR_001738847.3	n.1064+1981G>A		intron_variant	Intron 8 of 8
PECR	XR_007078552.1	n.1064+1981G>A		intron_variant	Intron 8 of 9
PECR	XR_007078553.1	n.1064+1981G>A		intron_variant	Intron 8 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PECR	ENST00000442122.5	n.*440+1981G>A		intron_variant	Intron 7 of 7	2		ENSP00000395512.1

Frequencies

GnomAD3 genomes AF: 0.723 AC: 109994 AN: 152068 Hom.: 39936 Cov.: 33

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.755

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.694

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.761

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.698

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.723 AC: 110097 AN: 152186 Hom.: 39983 Cov.: 33 AF XY: 0.723 AC XY: 53798 AN XY: 74380

African (AFR) AF: 0.770 AC: 31973 AN: 41514

American (AMR) AF: 0.756 AC: 11559 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2215 AN: 3470

East Asian (EAS) AF: 0.694 AC: 3594 AN: 5182

South Asian (SAS) AF: 0.641 AC: 3088 AN: 4818

European-Finnish (FIN) AF: 0.761 AC: 8048 AN: 10582

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.698 AC: 47467 AN: 68006

Other (OTH) AF: 0.697 AC: 1474 AN: 2114

Alfa AF: 0.716 Hom.: 5728

Bravo AF: 0.730

Asia WGS AF: 0.667 AC: 2322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.27
DANN	Benign	0.38
PhyloP100		-0.94

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs934154; hg19: chr2-216901933;