NM_001321142.2:c.*293T>A

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001321142.2(CIDEC):​c.*293T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CIDEC NM_001321142.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

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>A		3_prime_UTR	Exon 7 of 7	NP_001308071.1
	CIDEC	NM_001199623.2		c.*293T>A		3_prime_UTR	Exon 6 of 6	NP_001186552.1
	CIDEC	NM_001199551.2		c.*293T>A		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>A		3_prime_UTR	Exon 7 of 7	ENSP00000338642.2
	CIDEC	ENST00000383817.5	TSL:1	c.*293T>A		3_prime_UTR	Exon 6 of 6	ENSP00000373328.2
	CIDEC	ENST00000455015.6	TSL:1	c.*293T>A		3_prime_UTR	Exon 6 of 6	ENSP00000392975.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 442248 Hom.: 0 Cov.: 2 AF XY: 0.00 AC XY: 0 AN XY: 232162

African (AFR) AF: 0.00 AC: 0 AN: 12368

American (AMR) AF: 0.00 AC: 0 AN: 18656

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 13658

East Asian (EAS) AF: 0.00 AC: 0 AN: 30820

South Asian (SAS) AF: 0.00 AC: 0 AN: 44892

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 29210

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1936

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 264944

Other (OTH) AF: 0.00 AC: 0 AN: 25764

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.057
DANN	Benign	0.73
PhyloP100		-2.0

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;