Genetic Variant CIDEC:c.*37C>G (chr3-9867065-G-C) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000443115.1(CIDEC):c.*37C>G variant causes a splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 1,541,092 control chromosomes in the GnomAD database, including 29,955 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.15 ( 2550 hom., cov: 33)

Exomes 𝑓: 0.18 ( 27405 hom. )

Consequence

CIDEC
ENST00000443115.1 splice_region

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0330

Variant links:

Genes affected

CIDEC (HGNC:24229): (cell death inducing DFFA like effector c) This gene encodes a member of the cell death-inducing DNA fragmentation factor-like effector family. Members of this family play important roles in apoptosis. The encoded protein promotes lipid droplet formation in adipocytes and may mediate adipocyte apoptosis. This gene is regulated by insulin and its expression is positively correlated with insulin sensitivity. Mutations in this gene may contribute to insulin resistant diabetes. A pseudogene of this gene is located on the short arm of chromosome 3. Alternatively spliced transcript variants that encode different isoforms have been observed for this gene. [provided by RefSeq, Dec 2010]

CIDEC links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 3-9867065-G-C is Benign according to our data. Variant chr3-9867065-G-C is described in ClinVar as [Benign]. Clinvar id is 1226316.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CIDEC	NM_001321142.2 link	c.*69C>G		3_prime_UTR_variant	Exon 7 of 7	ENST00000336832.7	NP_001308071.1	Q96AQ7-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CIDEC	ENST00000336832 link	c.*69C>G		3_prime_UTR_variant	Exon 7 of 7	1	NM_001321142.2	ENSP00000338642.2		Q96AQ7-1

Frequencies

GnomAD3 genomes

AF:

0.146

AC:

22177

AN:

152192

Hom.:

2554

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0358

Gnomad AMI

AF:

0.150

Gnomad AMR

AF:

0.159

Gnomad ASJ

AF:

0.192

Gnomad EAS

AF:

0.597

Gnomad SAS

AF:

0.192

Gnomad FIN

AF:

0.131

Gnomad MID

AF:

0.168

Gnomad NFE

AF:

0.171

Gnomad OTH

AF:

0.161

GnomAD3 exomes

AF:

0.191

AC:

47864

AN:

250140

Hom.:

6414

AF XY:

0.192

AC XY:

26036

AN XY:

135602

show subpopulations

Gnomad AFR exome

AF:

0.0331

Gnomad AMR exome

AF:

0.177

Gnomad ASJ exome

AF:

0.185

Gnomad EAS exome

AF:

0.600

Gnomad SAS exome

AF:

0.178

Gnomad FIN exome

AF:

0.125

Gnomad NFE exome

AF:

0.169

Gnomad OTH exome

AF:

0.175

GnomAD4 exome

AF:

0.183

AC:

254038

AN:

1388782

Hom.:

27405

Cov.:

AF XY:

0.183

AC XY:

126987

AN XY:

694868

show subpopulations

Gnomad4 AFR exome

AF:

0.0307

Gnomad4 AMR exome

AF:

0.174

Gnomad4 ASJ exome

AF:

0.192

Gnomad4 EAS exome

AF:

0.603

Gnomad4 SAS exome

AF:

0.178

Gnomad4 FIN exome

AF:

0.133

Gnomad4 NFE exome

AF:

0.175

Gnomad4 OTH exome

AF:

0.185

GnomAD4 genome

AF:

0.146

AC:

22168

AN:

152310

Hom.:

2550

Cov.:

AF XY:

0.146

AC XY:

10861

AN XY:

74468

show subpopulations

Gnomad4 AFR

AF:

0.0357

Gnomad4 AMR

AF:

0.159

Gnomad4 ASJ

AF:

0.192

Gnomad4 EAS

AF:

0.597

Gnomad4 SAS

AF:

0.192

Gnomad4 FIN

AF:

0.131

Gnomad4 NFE

AF:

0.171

Gnomad4 OTH

AF:

0.159

Alfa

AF:

0.157

Hom.:

442

Bravo

AF:

0.145

Asia WGS

AF:

0.353

AC:

1225

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jun 18, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

1.4

DANN

Benign

0.42

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over