7-121048409-C-T

Position:

• chr7-121048409-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.540+1416C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.657 in 152,140 control chromosomes in the GnomAD database, including 35,617 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 0.66 (35617 hom., cov: 33)
• Consequence: CPED1 NM_024913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.289

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]

CPED1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CPED1	NM_024913.5	c.540+1416C>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.540+1416C>T		intron_variant		1	NM_024913.5	ENSP00000309772.5

Frequencies

GnomAD3 genomes AF: 0.658 AC: 100018 AN: 152022 Hom.: 35622 Cov.: 33

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.853

Gnomad AMR AF: 0.804

Gnomad ASJ AF: 0.760

Gnomad EAS AF: 0.777

Gnomad SAS AF: 0.760

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.693

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

GnomAD4 genome AF: 0.657 AC: 100020 AN: 152140 Hom.: 35617 Cov.: 33 AF XY: 0.661 AC XY: 49133 AN XY: 74364

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.805

Gnomad4 ASJ AF: 0.760

Gnomad4 EAS AF: 0.776

Gnomad4 SAS AF: 0.760

Gnomad4 FIN AF: 0.690

Gnomad4 NFE AF: 0.775

Gnomad4 OTH AF: 0.686

Alfa AF: 0.745 Hom.: 21586

Bravo AF: 0.652

Asia WGS AF: 0.665 AC: 2317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.7
DANN	Benign	0.75

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: rs2160010; hg19: chr7-120688463;