chr7-121124519-C-A

Variant names:

• chr7-121124519-C-A
• rs798948
• NM_024913.5:c.1061+46C>A

Variant summary

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

The NM_024913.5(CPED1):​c.1061+46C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.898 in 1,322,402 control chromosomes in the GnomAD database, including 533,691 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 0.90 (61196 hom., cov: 31)
  • Exomes 𝑓: 0.90 (472495 hom.)
• Consequence: CPED1 NM_024913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700
• Publications: 7 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.935 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CPED1	NM_024913.5	c.1061+46C>A		intron_variant	Intron 8 of 22	ENST00000310396.10	NP_079189.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CPED1	ENST00000310396.10	c.1061+46C>A		intron_variant	Intron 8 of 22	1	NM_024913.5	ENSP00000309772.5

Frequencies

GnomAD3 genomes AF: 0.897 AC: 136287 AN: 151996 Hom.: 61151 Cov.: 31

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.952

Gnomad AMR AF: 0.937

Gnomad ASJ AF: 0.958

Gnomad EAS AF: 0.957

Gnomad SAS AF: 0.833

Gnomad FIN AF: 0.860

Gnomad MID AF: 0.994

Gnomad NFE AF: 0.900

Gnomad OTH AF: 0.911

GnomAD2 exomes AF: 0.887 AC: 81553 AN: 91958 AF XY: 0.887

Gnomad AFR exome AF: 0.872

Gnomad AMR exome AF: 0.910

Gnomad ASJ exome AF: 0.962

Gnomad EAS exome AF: 0.940

Gnomad FIN exome AF: 0.855

Gnomad NFE exome AF: 0.894

Gnomad OTH exome AF: 0.887

GnomAD4 exome AF: 0.898 AC: 1051020 AN: 1170288 Hom.: 472495 Cov.: 17 AF XY: 0.897 AC XY: 514044 AN XY: 572996

African (AFR) AF: 0.879 AC: 21828 AN: 24820

American (AMR) AF: 0.926 AC: 15620 AN: 16860

Ashkenazi Jewish (ASJ) AF: 0.960 AC: 17999 AN: 18742

East Asian (EAS) AF: 0.963 AC: 28695 AN: 29790

South Asian (SAS) AF: 0.844 AC: 42887 AN: 50806

European-Finnish (FIN) AF: 0.856 AC: 34551 AN: 40366

Middle Eastern (MID) AF: 0.958 AC: 3978 AN: 4152

European-Non Finnish (NFE) AF: 0.899 AC: 842206 AN: 937216

Other (OTH) AF: 0.910 AC: 43256 AN: 47536

GnomAD4 genome AF: 0.897 AC: 136391 AN: 152114 Hom.: 61196 Cov.: 31 AF XY: 0.896 AC XY: 66613 AN XY: 74366

African (AFR) AF: 0.878 AC: 36440 AN: 41514

American (AMR) AF: 0.937 AC: 14324 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.958 AC: 3324 AN: 3468

East Asian (EAS) AF: 0.957 AC: 4956 AN: 5180

South Asian (SAS) AF: 0.833 AC: 4015 AN: 4818

European-Finnish (FIN) AF: 0.860 AC: 9063 AN: 10542

Middle Eastern (MID) AF: 0.993 AC: 292 AN: 294

European-Non Finnish (NFE) AF: 0.900 AC: 61187 AN: 67998

Other (OTH) AF: 0.912 AC: 1924 AN: 2110

Alfa AF: 0.890 Hom.: 7820

Bravo AF: 0.905

Asia WGS AF: 0.890 AC: 3085 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.50
PhyloP100		0.070
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: rs798948; hg19: chr7-120764573;