7-121099908-GTTTT-GTTT

Position:

• chr7-121099908-GTTTT-GTTT

Variant summary

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

The NM_024913.5(CPED1):​c.750-3delT 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 0.19 (2969 hom., cov: 0)
  • Exomes 𝑓: 0.35 (1515 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 (SAS) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CPED1	NM_024913.5	c.750-3delT		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.750-3delT		splice_region_variant, intron_variant		1	NM_024913.5	ENSP00000309772.5

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28104 AN: 148288 Hom.: 2971 Cov.: 0

Gnomad AFR AF: 0.0926

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.208

GnomAD3 exomes AF: 0.318 AC: 52970 AN: 166798 Hom.: 554 AF XY: 0.325 AC XY: 29456 AN XY: 90770

Gnomad AFR exome AF: 0.199

Gnomad AMR exome AF: 0.313

Gnomad ASJ exome AF: 0.424

Gnomad EAS exome AF: 0.300

Gnomad SAS exome AF: 0.355

Gnomad FIN exome AF: 0.260

Gnomad NFE exome AF: 0.327

Gnomad OTH exome AF: 0.339

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.347 AC: 387034 AN: 1114450 Hom.: 1515 Cov.: 0 AF XY: 0.349 AC XY: 193737 AN XY: 555802

Gnomad4 AFR exome AF: 0.247

Gnomad4 AMR exome AF: 0.291

Gnomad4 ASJ exome AF: 0.413

Gnomad4 EAS exome AF: 0.325

Gnomad4 SAS exome AF: 0.351

Gnomad4 FIN exome AF: 0.279

Gnomad4 NFE exome AF: 0.353

Gnomad4 OTH exome AF: 0.353

GnomAD4 genome AF: 0.189 AC: 28109 AN: 148368 Hom.: 2969 Cov.: 0 AF XY: 0.187 AC XY: 13521 AN XY: 72122

Gnomad4 AFR AF: 0.0927

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.207

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;