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GeneBe

7-121015835-G-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_024913.5(CPED1):c.420G>A(p.Gly140=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00106 in 1,555,386 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0054 ( 7 hom., cov: 33)
Exomes 𝑓: 0.00058 ( 5 hom. )

Consequence

CPED1
NM_024913.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.871
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 7-121015835-G-A is Benign according to our data. Variant chr7-121015835-G-A is described in ClinVar as [Benign]. Clinvar id is 717860.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.871 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00542 (826/152306) while in subpopulation AFR AF= 0.0189 (787/41562). AF 95% confidence interval is 0.0178. There are 7 homozygotes in gnomad4. There are 389 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 7 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CPED1NM_024913.5 linkuse as main transcriptc.420G>A p.Gly140= synonymous_variant 3/23 ENST00000310396.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CPED1ENST00000310396.10 linkuse as main transcriptc.420G>A p.Gly140= synonymous_variant 3/231 NM_024913.5 P1A4D0V7-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00541
AC:
824
AN:
152188
Hom.:
7
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0189
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00157
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.0000882
Gnomad OTH
AF:
0.00335
GnomAD3 exomes
AF:
0.00155
AC:
310
AN:
200562
Hom.:
4
AF XY:
0.00115
AC XY:
126
AN XY:
109720
show subpopulations
Gnomad AFR exome
AF:
0.0186
Gnomad AMR exome
AF:
0.00139
Gnomad ASJ exome
AF:
0.000407
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000180
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000918
Gnomad OTH exome
AF:
0.00112
GnomAD4 exome
AF:
0.000581
AC:
815
AN:
1403080
Hom.:
5
Cov.:
31
AF XY:
0.000526
AC XY:
366
AN XY:
695530
show subpopulations
Gnomad4 AFR exome
AF:
0.0198
Gnomad4 AMR exome
AF:
0.00141
Gnomad4 ASJ exome
AF:
0.0000419
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000933
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000496
Gnomad4 OTH exome
AF:
0.00166
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00542
AC:
826
AN:
152306
Hom.:
7
Cov.:
33
AF XY:
0.00522
AC XY:
389
AN XY:
74480
show subpopulations
Gnomad4 AFR
AF:
0.0189
Gnomad4 AMR
AF:
0.00157
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000882
Gnomad4 OTH
AF:
0.00332
Alfa
AF:
0.00318
Hom.:
0
Bravo
AF:
0.00604
Asia WGS
AF:
0.000866
AC:
3
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJul 23, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
Cadd
Benign
1.2
Dann
Benign
0.44

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs34283669; hg19: chr7-120655889; API