3-9867065-G-C

Position:

• chr3-9867065-G-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001321142.2(CIDEC):​c.*69C>G variant causes a 3 prime UTR 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. 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 NM_001321142.2 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.0330

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]

ACMG classification

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/exons	MANE	Protein	UniProt
CIDEC	NM_001321142.2	c.*69C>G		3_prime_UTR_variant	7/7	ENST00000336832.7	NP_001308071.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CIDEC	ENST00000336832.7	c.*69C>G		3_prime_UTR_variant	7/7	1	NM_001321142.2	ENSP00000338642	A1

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22177 AN: 152192 Hom.: 2554 Cov.: 33

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

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.: 25 AF XY: 0.183 AC XY: 126987 AN XY: 694868

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.: 33 AF XY: 0.146 AC XY: 10861 AN XY: 74468

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

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 18, 2021	- -

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

Other links and lift over

dbSNP: rs1053239; hg19: chr3-9908749;