7-121016574-C-T

Position:

• chr7-121016574-C-T

Variant summary

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

The NM_024913.5(CPED1):​c.433+726C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.793 in 152,082 control chromosomes in the GnomAD database, including 48,085 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 0.79 (48085 hom., cov: 31)
• Consequence: CPED1 NM_024913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.360

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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.916 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CPED1	NM_024913.5	c.433+726C>T		intron_variant		ENST00000310396.10	NP_079189.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CPED1	ENST00000310396.10	c.433+726C>T		intron_variant		1	NM_024913.5	ENSP00000309772	P1

Frequencies

GnomAD3 genomes AF: 0.793 AC: 120491 AN: 151964 Hom.: 48033 Cov.: 31

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.866

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.938

Gnomad SAS AF: 0.897

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.876

Gnomad NFE AF: 0.796

Gnomad OTH AF: 0.814

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

GnomAD4 genome AF: 0.793 AC: 120594 AN: 152082 Hom.: 48085 Cov.: 31 AF XY: 0.795 AC XY: 59081 AN XY: 74342

Gnomad4 AFR AF: 0.751

Gnomad4 AMR AF: 0.866

Gnomad4 ASJ AF: 0.817

Gnomad4 EAS AF: 0.938

Gnomad4 SAS AF: 0.898

Gnomad4 FIN AF: 0.701

Gnomad4 NFE AF: 0.796

Gnomad4 OTH AF: 0.807

Alfa AF: 0.785 Hom.: 6877

Bravo AF: 0.802

Asia WGS AF: 0.858 AC: 2984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.9
DANN	Benign	0.74

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: rs6973457; hg19: chr7-120656628;