rs7630877

Variant names:

• chr3-179943530-G-A
• rs7630877
• NM_016559.3:c.93+28064C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-179943530-G-A
• chr3-179943530-G-C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_016559.3(PEX5L):​c.93+28064C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.329 in 152,040 control chromosomes in the GnomAD database, including 8,425 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 0.33 (8425 hom., cov: 33)
• Consequence: PEX5L NM_016559.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164
• Publications: 23 publications found

Genes affected

PEX5L (HGNC:30024): (peroxisomal biogenesis factor 5 like) Enables peroxisome matrix targeting signal-1 binding activity and small GTPase binding activity. Predicted to be involved in protein import into peroxisome matrix, docking and regulation of cAMP-mediated signaling. Predicted to act upstream of or within maintenance of protein location and regulation of membrane potential. Located in cytosol. Part of receptor complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016559.3. 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
	PEX5L	NM_016559.3	MANE Select	c.93+28064C>T		intron	N/A	NP_057643.1	Q8IYB4-1
	PEX5L	NM_001349386.2		c.258+28064C>T		intron	N/A	NP_001336315.1
	PEX5L	NM_001349387.2		c.165+28064C>T		intron	N/A	NP_001336316.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PEX5L	ENST00000467460.6	TSL:1 MANE Select	c.93+28064C>T		intron	N/A	ENSP00000419975.1	Q8IYB4-1
	PEX5L	ENST00000263962.12	TSL:1	c.22-42795C>T		intron	N/A	ENSP00000263962.8	Q8IYB4-2
	PEX5L	ENST00000485199.5	TSL:1	c.93+28064C>T		intron	N/A	ENSP00000418440.1	Q8IYB4-3

Frequencies

GnomAD3 genomes AF: 0.329 AC: 50032 AN: 151922 Hom.: 8409 Cov.: 33

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.329 AC: 50071 AN: 152040 Hom.: 8425 Cov.: 33 AF XY: 0.328 AC XY: 24353 AN XY: 74304

African (AFR) AF: 0.353 AC: 14657 AN: 41470

American (AMR) AF: 0.243 AC: 3719 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.468 AC: 1625 AN: 3470

East Asian (EAS) AF: 0.158 AC: 819 AN: 5180

South Asian (SAS) AF: 0.303 AC: 1459 AN: 4818

European-Finnish (FIN) AF: 0.358 AC: 3780 AN: 10550

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.336 AC: 22856 AN: 67956

Other (OTH) AF: 0.351 AC: 740 AN: 2110

Alfa AF: 0.333 Hom.: 39691

Bravo AF: 0.320

Asia WGS AF: 0.264 AC: 917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	2.4
DANN	Benign	0.68
PhyloP100		-0.16
Mutation Taster		=100/0	polymorphism (auto)

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: rs7630877; hg19: chr3-179661318;