rs12706309

Positions:

• chr7-121055373-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024913.5(CPED1):​c.540+8380T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.657 in 151,814 control chromosomes in the GnomAD database, including 35,527 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 0.66 (35527 hom., cov: 33)
• Consequence: CPED1 NM_024913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.583

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CPED1	NM_024913.5	c.540+8380T>G		intron_variant		ENST00000310396.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CPED1	ENST00000310396.10	c.540+8380T>G		intron_variant		1	NM_024913.5	P1
CPED1	ENST00000450913.6	c.540+8380T>G		intron_variant		1
CPED1	ENST00000428526.5	c.540+8380T>G		intron_variant		2
CPED1	ENST00000520801.5	c.*177+8380T>G		intron_variant, NMD_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.658 AC: 99766 AN: 151696 Hom.: 35532 Cov.: 33

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.853

Gnomad AMR AF: 0.805

Gnomad ASJ AF: 0.759

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.775

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.657 AC: 99768 AN: 151814 Hom.: 35527 Cov.: 33 AF XY: 0.660 AC XY: 49018 AN XY: 74230

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.805

Gnomad4 ASJ AF: 0.759

Gnomad4 EAS AF: 0.775

Gnomad4 SAS AF: 0.761

Gnomad4 FIN AF: 0.689

Gnomad4 NFE AF: 0.775

Gnomad4 OTH AF: 0.685

Alfa AF: 0.694 Hom.: 4805

Bravo AF: 0.652

Asia WGS AF: 0.665 AC: 2287 AN: 3436

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	7.2
DANN	Benign	0.53

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

Publications

LitVar

Other links and lift over

dbSNP: rs12706309; hg19: chr7-120695427;