NM_024913.5:c.616+12170T>C

Variant names:

• chr7-121076483-T-C
• rs10275526
• NM_024913.5:c.616+12170T>C

Variant summary

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

The NM_024913.5(CPED1):​c.616+12170T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.462 in 151,980 control chromosomes in the GnomAD database, including 16,496 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 0.46 (16496 hom., cov: 31)
  • Exomes 𝑓: 0.33 (0 hom.)
• Consequence: CPED1 NM_024913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.571
• Publications: 5 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=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.593 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPED1	NM_024913.5	MANE Select	c.616+12170T>C		intron	N/A	NP_079189.4
	CPED1	NM_001105533.1		c.616+12170T>C		intron	N/A	NP_001099003.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPED1	ENST00000310396.10	TSL:1 MANE Select	c.616+12170T>C		intron	N/A	ENSP00000309772.5
	CPED1	ENST00000450913.6	TSL:1	c.616+12170T>C		intron	N/A	ENSP00000406122.2
	CPED1	ENST00000423795.5	TSL:1	c.-45+12170T>C		intron	N/A	ENSP00000415573.1

Frequencies

GnomAD3 genomes AF: 0.462 AC: 70134 AN: 151850 Hom.: 16492 Cov.: 31

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.702

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.487

GnomAD4 exome AF: 0.333 AC: 4 AN: 12 Hom.: 0 AF XY: 0.375 AC XY: 3 AN XY: 8

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.300 AC: 3 AN: 10

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.462 AC: 70177 AN: 151968 Hom.: 16496 Cov.: 31 AF XY: 0.468 AC XY: 34792 AN XY: 74296

African (AFR) AF: 0.441 AC: 18284 AN: 41450

American (AMR) AF: 0.590 AC: 9020 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1520 AN: 3464

East Asian (EAS) AF: 0.611 AC: 3147 AN: 5150

South Asian (SAS) AF: 0.373 AC: 1795 AN: 4808

European-Finnish (FIN) AF: 0.470 AC: 4979 AN: 10584

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.436 AC: 29623 AN: 67926

Other (OTH) AF: 0.482 AC: 1015 AN: 2104

Alfa AF: 0.421 Hom.: 7305

Bravo AF: 0.473

Asia WGS AF: 0.462 AC: 1608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	1.3
DANN	Benign	0.65
PhyloP100		-0.57
PromoterAI		0.054	Neutral
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: rs10275526; hg19: chr7-120716537;