chr7-121016574-C-T

Variant names:

• chr7-121016574-C-T
• rs6973457
• NM_024913.5:c.433+726C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024913.5(CPED1):​c.433+726C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.793 in 152,082 control chromosomes in the GnomAD database, including 48,085 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.79 (48085 hom., cov: 31)
• Consequence: CPED1 NM_024913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.360
• Publications: 1 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.916 is higher than 0.05.

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.433+726C>T		intron	N/A	NP_079189.4
	CPED1	NM_001105533.1		c.433+726C>T		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.433+726C>T		intron	N/A	ENSP00000309772.5
	CPED1	ENST00000450913.6	TSL:1	c.433+726C>T		intron	N/A	ENSP00000406122.2
	CPED1	ENST00000495036.5	TSL:1	n.880+726C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.793 AC: 120491 AN: 151964 Hom.: 48033 Cov.: 31

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.866

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.938

Gnomad SAS AF: 0.897

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.876

Gnomad NFE AF: 0.796

Gnomad OTH AF: 0.814

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.793 AC: 120594 AN: 152082 Hom.: 48085 Cov.: 31 AF XY: 0.795 AC XY: 59081 AN XY: 74342

African (AFR) AF: 0.751 AC: 31158 AN: 41498

American (AMR) AF: 0.866 AC: 13228 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.817 AC: 2836 AN: 3470

East Asian (EAS) AF: 0.938 AC: 4852 AN: 5170

South Asian (SAS) AF: 0.898 AC: 4327 AN: 4820

European-Finnish (FIN) AF: 0.701 AC: 7396 AN: 10550

Middle Eastern (MID) AF: 0.873 AC: 255 AN: 292

European-Non Finnish (NFE) AF: 0.796 AC: 54095 AN: 67982

Other (OTH) AF: 0.807 AC: 1704 AN: 2112

Alfa AF: 0.785 Hom.: 6877

Bravo AF: 0.802

Asia WGS AF: 0.858 AC: 2984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.9
DANN	Benign	0.74
PhyloP100		0.36
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: rs6973457; hg19: chr7-120656628;