chr7-121099908-GTTT-G

Position:

• chr7-121099908-GTTT-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BS1

The NM_024913.5(CPED1):​c.750-5_750-3delTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00767 in 1,464,776 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.00046 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0085 (0 hom.)
• 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 Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BS1: Variant frequency is greater than expected in population amr. gnomad4_exome allele frequency = 0.00849 (11168/1316006) while in subpopulation AMR AF= 0.0185 (672/36306). AF 95% confidence interval is 0.0173. There are 0 homozygotes in gnomad4_exome. There are 5424 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CPED1	NM_024913.5	c.750-5_750-3delTTT		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.750-5_750-3delTTT		splice_region_variant, intron_variant		1	NM_024913.5	ENSP00000309772.5

Frequencies

GnomAD3 genomes AF: 0.000457 AC: 68 AN: 148686 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000222

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000134

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000786

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000516

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000686

Gnomad OTH AF: 0.000985

GnomAD3 exomes AF: 0.0162 AC: 2704 AN: 166798 Hom.: 0 AF XY: 0.0162 AC XY: 1468 AN XY: 90770

Gnomad AFR exome AF: 0.0138

Gnomad AMR exome AF: 0.0258

Gnomad ASJ exome AF: 0.0160

Gnomad EAS exome AF: 0.0185

Gnomad SAS exome AF: 0.00935

Gnomad FIN exome AF: 0.0193

Gnomad NFE exome AF: 0.0153

Gnomad OTH exome AF: 0.0147

GnomAD4 exome AF: 0.00849 AC: 11168 AN: 1316006 Hom.: 0 AF XY: 0.00826 AC XY: 5424 AN XY: 656298

Gnomad4 AFR exome AF: 0.0121

Gnomad4 AMR exome AF: 0.0185

Gnomad4 ASJ exome AF: 0.00984

Gnomad4 EAS exome AF: 0.0104

Gnomad4 SAS exome AF: 0.00720

Gnomad4 FIN exome AF: 0.0128

Gnomad4 NFE exome AF: 0.00780

Gnomad4 OTH exome AF: 0.00922

GnomAD4 genome AF: 0.000464 AC: 69 AN: 148770 Hom.: 0 Cov.: 0 AF XY: 0.000442 AC XY: 32 AN XY: 72360

Gnomad4 AFR AF: 0.000246

Gnomad4 AMR AF: 0.000133

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000788

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000516

Gnomad4 NFE AF: 0.000686

Gnomad4 OTH AF: 0.000976

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;