chrX-18724524-G-A

Variant names:

• chrX-18724524-G-A
• rs6633130
• NM_001377996.1:c.47-5657G>A

Variant summary

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

The NM_001377996.1(PPEF1):​c.47-5657G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.068 in 111,976 control chromosomes in the GnomAD database, including 654 homozygotes. There are 2,097 hemizygotes in GnomAD. 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 0.068 (654 hom., 2097 hem., cov: 23)
• Consequence: PPEF1 NM_001377996.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.816
• Publications: 1 publications found

Genes affected

PPEF1 (HGNC:9243): (protein phosphatase with EF-hand domain 1) This gene encodes a member of the serine/threonine protein phosphatase with EF-hand motif family. The protein contains a protein phosphatase catalytic domain, and at least two EF-hand calcium-binding motifs in its C terminus. Although its substrate(s) is unknown, the encoded protein has been suggested to play a role in specific sensory neuron function and/or development. This gene shares high sequence similarity with the Drosophila retinal degeneration C (rdgC) gene. Several alternatively spliced transcript variants, each encoding a distinct isoform, have been described. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001377996.1. 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
	PPEF1	NM_001377996.1	MANE Select	c.47-5657G>A		intron	N/A	NP_001364925.1
	PPEF1	NM_001377986.2		c.47-5657G>A		intron	N/A	NP_001364915.1
	PPEF1	NM_001377993.1		c.47-5657G>A		intron	N/A	NP_001364922.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPEF1	ENST00000470157.2	TSL:3 MANE Select	c.47-5657G>A		intron	N/A	ENSP00000419273.2
	PPEF1	ENST00000361511.9	TSL:1	c.47-5657G>A		intron	N/A	ENSP00000354871.3
	PPEF1	ENST00000471570.6	TSL:3	c.47-5657G>A		intron	N/A	ENSP00000509623.1

Frequencies

GnomAD3 genomes AF: 0.0680 AC: 7608 AN: 111925 Hom.: 655 Cov.: 23

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0312

Gnomad ASJ AF: 0.000378

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00112

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0128

Gnomad NFE AF: 0.000620

Gnomad OTH AF: 0.0561

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

GnomAD4 genome AF: 0.0680 AC: 7612 AN: 111976 Hom.: 654 Cov.: 23 AF XY: 0.0613 AC XY: 2097 AN XY: 34208

African (AFR) AF: 0.233 AC: 7159 AN: 30709

American (AMR) AF: 0.0312 AC: 330 AN: 10582

Ashkenazi Jewish (ASJ) AF: 0.000378 AC: 1 AN: 2645

East Asian (EAS) AF: 0.00 AC: 0 AN: 3560

South Asian (SAS) AF: 0.000752 AC: 2 AN: 2661

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6129

Middle Eastern (MID) AF: 0.00935 AC: 2 AN: 214

European-Non Finnish (NFE) AF: 0.000620 AC: 33 AN: 53258

Other (OTH) AF: 0.0554 AC: 85 AN: 1533

Alfa AF: 0.0339 Hom.: 2727

Bravo AF: 0.0799

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	11
DANN	Benign	0.88
PhyloP100		0.82
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: rs6633130; hg19: chrX-18742642;