chr7-121099908-GTT-G

Position:

• chr7-121099908-GTT-G

Variant summary

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

The NM_024913.5(CPED1):​c.750-4_750-3delTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.70 (36378 hom., cov: 0)
  • Exomes 𝑓: 0.47 (33747 hom.)
  • Failed GnomAD Quality Control
• Consequence: CPED1 NM_024913.5 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29

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 = 0.82 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CPED1	NM_024913.5	c.750-4_750-3delTT		splice_region_variant, intron_variant		ENST00000310396.10	NP_079189.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CPED1	ENST00000310396.10	c.750-4_750-3delTT		splice_region_variant, intron_variant		1	NM_024913.5	ENSP00000309772.5

Frequencies

GnomAD3 genomes AF: 0.698 AC: 103823 AN: 148648 Hom.: 36346 Cov.: 0

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.779

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.842

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.698

GnomAD3 exomes AF: 0.502 AC: 83747 AN: 166798 Hom.: 10314 AF XY: 0.492 AC XY: 44638 AN XY: 90770

Gnomad AFR exome AF: 0.593

Gnomad AMR exome AF: 0.528

Gnomad ASJ exome AF: 0.448

Gnomad EAS exome AF: 0.590

Gnomad SAS exome AF: 0.405

Gnomad FIN exome AF: 0.531

Gnomad NFE exome AF: 0.498

Gnomad OTH exome AF: 0.489

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.465 AC: 622606 AN: 1338460 Hom.: 33747 AF XY: 0.463 AC XY: 309215 AN XY: 667588

Gnomad4 AFR exome AF: 0.510

Gnomad4 AMR exome AF: 0.522

Gnomad4 ASJ exome AF: 0.455

Gnomad4 EAS exome AF: 0.532

Gnomad4 SAS exome AF: 0.409

Gnomad4 FIN exome AF: 0.487

Gnomad4 NFE exome AF: 0.462

Gnomad4 OTH exome AF: 0.469

GnomAD4 genome AF: 0.699 AC: 103899 AN: 148734 Hom.: 36378 Cov.: 0 AF XY: 0.700 AC XY: 50609 AN XY: 72334

Gnomad4 AFR AF: 0.767

Gnomad4 AMR AF: 0.779

Gnomad4 ASJ AF: 0.620

Gnomad4 EAS AF: 0.842

Gnomad4 SAS AF: 0.544

Gnomad4 FIN AF: 0.671

Gnomad4 NFE AF: 0.646

Gnomad4 OTH AF: 0.701

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: rs33990520; hg19: chr7-120739962;