7-121062691-TC-T

Position:

• chr7-121062691-TC-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_024913.5(CPED1):​c.541-1543del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.666 in 151,952 control chromosomes in the GnomAD database, including 35,266 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.67 (35264 hom., cov: 0)
  • Exomes 𝑓: 1.0 (2 hom.)
• Consequence: CPED1 NM_024913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.906 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CPED1	NM_024913.5	c.541-1543del		intron_variant		ENST00000310396.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CPED1	ENST00000310396.10	c.541-1543del		intron_variant		1	NM_024913.5	P1
CPED1	ENST00000450913.6	c.541-1543del		intron_variant		1
CPED1	ENST00000428526.5	c.541-1543del		intron_variant		2
CPED1	ENST00000520801.5	c.*178-1543del		intron_variant, NMD_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.666 AC: 101169 AN: 151830 Hom.: 35267 Cov.: 0

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.890

Gnomad AMR AF: 0.813

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.929

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.736

Gnomad OTH AF: 0.723

GnomAD4 exome AF: 1.00 AC: 4 AN: 4 Hom.: 2 AF XY: 1.00 AC XY: 2 AN XY: 2

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.666 AC: 101186 AN: 151948 Hom.: 35264 Cov.: 0 AF XY: 0.664 AC XY: 49351 AN XY: 74286

Gnomad4 AFR AF: 0.464

Gnomad4 AMR AF: 0.813

Gnomad4 ASJ AF: 0.783

Gnomad4 EAS AF: 0.928

Gnomad4 SAS AF: 0.716

Gnomad4 FIN AF: 0.570

Gnomad4 NFE AF: 0.736

Gnomad4 OTH AF: 0.716

Alfa AF: 0.680 Hom.: 4433

Bravo AF: 0.679

Asia WGS AF: 0.730 AC: 2539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs36113801; hg19: chr7-120702745;