chr7-121263761-A-T

Variant names:

• chr7-121263761-A-T
• rs4609139
• NM_024913.5:c.2311-2466A>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.2311-2466A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 151,828 control chromosomes in the GnomAD database, including 7,702 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 0.31 (7702 hom., cov: 32)
• Consequence: CPED1 NM_024913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• Publications: 17 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 = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CPED1	NM_024913.5	c.2311-2466A>T		intron_variant	Intron 18 of 22	ENST00000310396.10	NP_079189.4
CPED1	XM_024446941.2	c.1798-2466A>T		intron_variant	Intron 16 of 20		XP_024302709.1
LOC124901735	XR_007060494.1	n.64+2900T>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CPED1	ENST00000310396.10	c.2311-2466A>T		intron_variant	Intron 18 of 22	1	NM_024913.5	ENSP00000309772.5

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47363 AN: 151710 Hom.: 7691 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.312 AC: 47402 AN: 151828 Hom.: 7702 Cov.: 32 AF XY: 0.309 AC XY: 22902 AN XY: 74178

African (AFR) AF: 0.270 AC: 11166 AN: 41404

American (AMR) AF: 0.262 AC: 4001 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.422 AC: 1463 AN: 3468

East Asian (EAS) AF: 0.126 AC: 649 AN: 5140

South Asian (SAS) AF: 0.351 AC: 1687 AN: 4812

European-Finnish (FIN) AF: 0.301 AC: 3181 AN: 10554

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.356 AC: 24165 AN: 67882

Other (OTH) AF: 0.334 AC: 707 AN: 2114

Alfa AF: 0.326 Hom.: 1040

Bravo AF: 0.306

Asia WGS AF: 0.289 AC: 1007 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	2.4
DANN	Benign	0.71
PhyloP100		-0.54
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: rs4609139; hg19: chr7-120903815;