7-121055438-A-G

Variant names:

• chr7-121055438-A-G
• rs10085563
• NM_024913.5:c.540+8445A>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.540+8445A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.69 in 151,686 control chromosomes in the GnomAD database, including 37,707 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 0.69 (37707 hom., cov: 32)
• Consequence: CPED1 NM_024913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 2 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.807 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.540+8445A>G		intron	N/A	NP_079189.4
	CPED1	NM_001105533.1		c.540+8445A>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.540+8445A>G		intron	N/A	ENSP00000309772.5
	CPED1	ENST00000450913.6	TSL:1	c.540+8445A>G		intron	N/A	ENSP00000406122.2
	CPED1	ENST00000428526.5	TSL:2	c.540+8445A>G		intron	N/A	ENSP00000398082.1

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104587 AN: 151568 Hom.: 37699 Cov.: 32

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.853

Gnomad AMR AF: 0.819

Gnomad ASJ AF: 0.761

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.776

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.690 AC: 104628 AN: 151686 Hom.: 37707 Cov.: 32 AF XY: 0.692 AC XY: 51261 AN XY: 74116

African (AFR) AF: 0.471 AC: 19516 AN: 41414

American (AMR) AF: 0.819 AC: 12503 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.761 AC: 2643 AN: 3472

East Asian (EAS) AF: 0.775 AC: 4009 AN: 5176

South Asian (SAS) AF: 0.761 AC: 3672 AN: 4824

European-Finnish (FIN) AF: 0.690 AC: 7176 AN: 10402

Middle Eastern (MID) AF: 0.738 AC: 214 AN: 290

European-Non Finnish (NFE) AF: 0.776 AC: 52613 AN: 67828

Other (OTH) AF: 0.713 AC: 1504 AN: 2108

Alfa AF: 0.741 Hom.: 9787

Bravo AF: 0.689

Asia WGS AF: 0.675 AC: 2325 AN: 3440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.19
DANN	Benign	0.60
PhyloP100		-1.6
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: rs10085563; hg19: chr7-120695492;