2-216037210-C-T

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000442122.5. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PECR	ENST00000442122.5	TSL:2	n.*440+1981G>A		intron	N/A	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 v4.9

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;