7-121099908-GTTTTTTT-GTTTTT

Variant names:

• chr7-121099908-GTT-G
• rs33990520
• NM_024913.5:c.750-4_750-3delTT

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CPED1	NM_024913.5	c.750-4_750-3delTT		splice_region_variant, intron_variant	Intron 6 of 22	ENST00000310396.10	NP_079189.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CPED1	ENST00000310396.10	c.750-17_750-16delTT		intron_variant	Intron 6 of 22	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

GnomAD2 exomes AF: 0.502 AC: 83747 AN: 166798 AF XY: 0.492

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 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

African (AFR) AF: 0.510 AC: 15158 AN: 29728

American (AMR) AF: 0.522 AC: 19594 AN: 37570

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 10846 AN: 23852

East Asian (EAS) AF: 0.532 AC: 19707 AN: 37020

South Asian (SAS) AF: 0.409 AC: 32305 AN: 78906

European-Finnish (FIN) AF: 0.487 AC: 22728 AN: 46704

Middle Eastern (MID) AF: 0.541 AC: 2902 AN: 5366

European-Non Finnish (NFE) AF: 0.462 AC: 473380 AN: 1023928

Other (OTH) AF: 0.469 AC: 25986 AN: 55386

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

African (AFR) AF: 0.767 AC: 31121 AN: 40578

American (AMR) AF: 0.779 AC: 11678 AN: 14992

Ashkenazi Jewish (ASJ) AF: 0.620 AC: 2130 AN: 3438

East Asian (EAS) AF: 0.842 AC: 4270 AN: 5074

South Asian (SAS) AF: 0.544 AC: 2541 AN: 4674

European-Finnish (FIN) AF: 0.671 AC: 6513 AN: 9700

Middle Eastern (MID) AF: 0.727 AC: 205 AN: 282

European-Non Finnish (NFE) AF: 0.646 AC: 43310 AN: 67036

Other (OTH) AF: 0.701 AC: 1438 AN: 2050

Alfa AF: 0.489 Hom.: 136

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.3
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs33990520; hg19: chr7-120739962;