chr7-121107254-T-G

Variant names:

• chr7-121107254-T-G
• rs13223036
• NM_024913.5:c.918+7160T>G

Variant summary

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

The NM_024913.5(CPED1):​c.918+7160T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 152,032 control chromosomes in the GnomAD database, including 6,839 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 0.29 (6839 hom., cov: 32)
• Consequence: CPED1 NM_024913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.335
• 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]

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 (SAS) allele frequency at 95% confidence interval = 0.346 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.918+7160T>G		intron	N/A	NP_079189.4
	CPED1	NM_001105533.1		c.918+7160T>G		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.918+7160T>G		intron	N/A	ENSP00000309772.5
	CPED1	ENST00000450913.6	TSL:1	c.918+7160T>G		intron	N/A	ENSP00000406122.2
	CPED1	ENST00000423795.5	TSL:1	c.258+7160T>G		intron	N/A	ENSP00000415573.1

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44110 AN: 151914 Hom.: 6837 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.290 AC: 44125 AN: 152032 Hom.: 6839 Cov.: 32 AF XY: 0.286 AC XY: 21279 AN XY: 74316

African (AFR) AF: 0.222 AC: 9208 AN: 41470

American (AMR) AF: 0.241 AC: 3679 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1529 AN: 3466

East Asian (EAS) AF: 0.126 AC: 654 AN: 5176

South Asian (SAS) AF: 0.357 AC: 1721 AN: 4824

European-Finnish (FIN) AF: 0.246 AC: 2605 AN: 10594

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.349 AC: 23746 AN: 67950

Other (OTH) AF: 0.302 AC: 634 AN: 2102

Alfa AF: 0.323 Hom.: 10703

Bravo AF: 0.287

Asia WGS AF: 0.256 AC: 892 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.81
DANN	Benign	0.56
PhyloP100		-0.34
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: rs13223036; hg19: chr7-120747308;