7-121203462-C-T

Variant names:

• chr7-121203462-C-T
• rs7797976
• NM_024913.5:c.2056-33252C>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.2056-33252C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 151,974 control chromosomes in the GnomAD database, including 9,743 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 0.35 (9743 hom., cov: 32)
• Consequence: CPED1 NM_024913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137
• Publications: 14 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]

LOC124901735 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CPED1	NM_024913.5	c.2056-33252C>T		intron_variant	Intron 16 of 22	ENST00000310396.10	NP_079189.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CPED1	ENST00000310396.10	c.2056-33252C>T		intron_variant	Intron 16 of 22	1	NM_024913.5	ENSP00000309772.5
CPED1	ENST00000450913.6	c.2056-33252C>T		intron_variant	Intron 15 of 17	1		ENSP00000406122.2
CPED1	ENST00000423795.5	c.1396-33252C>T		intron_variant	Intron 13 of 15	1		ENSP00000415573.1
CPED1	ENST00000466055.1	n.89-33252C>T		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53186 AN: 151854 Hom.: 9739 Cov.: 32

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.350 AC: 53217 AN: 151974 Hom.: 9743 Cov.: 32 AF XY: 0.346 AC XY: 25713 AN XY: 74290

African (AFR) AF: 0.304 AC: 12615 AN: 41444

American (AMR) AF: 0.280 AC: 4270 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1712 AN: 3460

East Asian (EAS) AF: 0.116 AC: 598 AN: 5146

South Asian (SAS) AF: 0.371 AC: 1785 AN: 4812

European-Finnish (FIN) AF: 0.317 AC: 3359 AN: 10582

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.407 AC: 27645 AN: 67944

Other (OTH) AF: 0.358 AC: 755 AN: 2108

Alfa AF: 0.368 Hom.: 1339

Bravo AF: 0.344

Asia WGS AF: 0.280 AC: 977 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.9
DANN	Benign	0.63
PhyloP100		0.14
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: rs7797976; hg19: chr7-120843516;