7-121055438-A-G

Position:

• chr7-121055438-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024913.5(CPED1):​c.540+8445A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.69 in 151,686 control chromosomes in the GnomAD database, including 37,707 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 0.69 (37707 hom., cov: 32)
• Consequence: CPED1 NM_024913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56

Genes affected

CPED1 (HGNC:26159): (cadherin like and PC-esterase domain containing 1) Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.807 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CPED1	NM_024913.5	c.540+8445A>G		intron_variant		ENST00000310396.10	NP_079189.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CPED1	ENST00000310396.10	c.540+8445A>G		intron_variant		1	NM_024913.5	ENSP00000309772.5
CPED1	ENST00000450913.6	c.540+8445A>G		intron_variant		1		ENSP00000406122.2
CPED1	ENST00000428526.5	c.540+8445A>G		intron_variant		2		ENSP00000398082.1
CPED1	ENST00000520801.5	n.*177+8445A>G		intron_variant		4		ENSP00000428504.1

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104587 AN: 151568 Hom.: 37699 Cov.: 32

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.853

Gnomad AMR AF: 0.819

Gnomad ASJ AF: 0.761

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.776

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.690 AC: 104628 AN: 151686 Hom.: 37707 Cov.: 32 AF XY: 0.692 AC XY: 51261 AN XY: 74116

Gnomad4 AFR AF: 0.471

Gnomad4 AMR AF: 0.819

Gnomad4 ASJ AF: 0.761

Gnomad4 EAS AF: 0.775

Gnomad4 SAS AF: 0.761

Gnomad4 FIN AF: 0.690

Gnomad4 NFE AF: 0.776

Gnomad4 OTH AF: 0.713

Alfa AF: 0.741 Hom.: 9787

Bravo AF: 0.689

Asia WGS AF: 0.675 AC: 2325 AN: 3440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.19
DANN	Benign	0.60

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

LitVar

Other links and lift over

dbSNP: rs10085563; hg19: chr7-120695492;