7-121099908-GTTTTTTT-G

Variant names:

• chr7-121099908-GTTTTTTT-G
• rs33990520
• NM_024913.5:c.750-9_750-3delTTTTTTT

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_024913.5(CPED1):​c.750-9_750-3delTTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000742 in 1,346,868 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 7.4e-7 (0 hom.)
• Consequence: CPED1 NM_024913.5 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.48
• Publications: 0 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: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024913.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPED1	NM_024913.5	MANE Select	c.750-9_750-3delTTTTTTT		splice_region intron	N/A	NP_079189.4
	CPED1	NM_001105533.1		c.750-9_750-3delTTTTTTT		splice_region intron	N/A	NP_001099003.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPED1	ENST00000310396.10	TSL:1 MANE Select	c.750-17_750-11delTTTTTTT		intron	N/A	ENSP00000309772.5
	CPED1	ENST00000450913.6	TSL:1	c.750-17_750-11delTTTTTTT		intron	N/A	ENSP00000406122.2
	CPED1	ENST00000423795.5	TSL:1	c.90-17_90-11delTTTTTTT		intron	N/A	ENSP00000415573.1

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome AF: 7.42e-7 AC: 1 AN: 1346868 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 671652

African (AFR) AF: 0.00 AC: 0 AN: 29856

American (AMR) AF: 0.00 AC: 0 AN: 37658

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 24014

East Asian (EAS) AF: 0.00 AC: 0 AN: 37084

South Asian (SAS) AF: 0.00 AC: 0 AN: 79552

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 46908

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5398

European-Non Finnish (NFE) AF: 9.70e-7 AC: 1 AN: 1030698

Other (OTH) AF: 0.00 AC: 0 AN: 55700

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.5

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs33990520; hg19: chr7-120739962;