NM_001321142.2:c.*293T>C

Variant names:

• chr3-9866841-A-G
• rs2479
• NM_001321142.2:c.*293T>C

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001321142.2(CIDEC):​c.*293T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.793 in 594,160 control chromosomes in the GnomAD database, including 187,210 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.79 (47730 hom., cov: 32)
  • Exomes 𝑓: 0.79 (139480 hom.)
• Consequence: CIDEC NM_001321142.2 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -1.97
• Publications: 17 publications found

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 Gene-Disease associations (from GenCC):

• CIDEC-related familial partial lipodystrophy

  Inheritance: Unknown, AR Classification: SUPPORTIVE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Orphanet

ENSG00000308530 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 3-9866841-A-G is Benign according to our data. Variant chr3-9866841-A-G is described in ClinVar as Benign. ClinVar VariationId is 1263470.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.802 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001321142.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CIDEC	NM_001321142.2	MANE Select	c.*293T>C		3_prime_UTR	Exon 7 of 7	NP_001308071.1
	CIDEC	NM_001199623.2		c.*293T>C		3_prime_UTR	Exon 6 of 6	NP_001186552.1
	CIDEC	NM_001199551.2		c.*293T>C		3_prime_UTR	Exon 7 of 7	NP_001186480.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CIDEC	ENST00000336832.7	TSL:1 MANE Select	c.*293T>C		3_prime_UTR	Exon 7 of 7	ENSP00000338642.2
	CIDEC	ENST00000383817.5	TSL:1	c.*293T>C		3_prime_UTR	Exon 6 of 6	ENSP00000373328.2
	CIDEC	ENST00000455015.6	TSL:1	c.*293T>C		3_prime_UTR	Exon 6 of 6	ENSP00000392975.1

Frequencies

GnomAD3 genomes AF: 0.791 AC: 120323 AN: 152050 Hom.: 47688 Cov.: 32

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.799

Gnomad EAS AF: 0.760

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.764

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.807

Gnomad OTH AF: 0.790

GnomAD4 exome AF: 0.793 AC: 350634 AN: 441992 Hom.: 139480 Cov.: 2 AF XY: 0.795 AC XY: 184321 AN XY: 231996

African (AFR) AF: 0.805 AC: 9953 AN: 12366

American (AMR) AF: 0.685 AC: 12763 AN: 18644

Ashkenazi Jewish (ASJ) AF: 0.788 AC: 10760 AN: 13656

East Asian (EAS) AF: 0.755 AC: 23244 AN: 30804

South Asian (SAS) AF: 0.803 AC: 36046 AN: 44864

European-Finnish (FIN) AF: 0.759 AC: 22157 AN: 29196

Middle Eastern (MID) AF: 0.811 AC: 1568 AN: 1934

European-Non Finnish (NFE) AF: 0.807 AC: 213630 AN: 264780

Other (OTH) AF: 0.797 AC: 20513 AN: 25748

GnomAD4 genome AF: 0.791 AC: 120416 AN: 152168 Hom.: 47730 Cov.: 32 AF XY: 0.788 AC XY: 58619 AN XY: 74396

African (AFR) AF: 0.799 AC: 33161 AN: 41488

American (AMR) AF: 0.723 AC: 11053 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.799 AC: 2775 AN: 3472

East Asian (EAS) AF: 0.759 AC: 3932 AN: 5178

South Asian (SAS) AF: 0.803 AC: 3876 AN: 4826

European-Finnish (FIN) AF: 0.764 AC: 8092 AN: 10594

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.807 AC: 54883 AN: 67994

Other (OTH) AF: 0.794 AC: 1678 AN: 2114

Alfa AF: 0.799 Hom.: 154146

Bravo AF: 0.786

Asia WGS AF: 0.822 AC: 2859 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

Nov 10, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.065
DANN	Benign	0.54
PhyloP100		-2.0
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: rs2479; hg19: chr3-9908525;