3-9866841-A-G

Position:

• chr3-9866841-A-G

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.*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

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 3-9866841-A-G is Benign according to our data. Variant chr3-9866841-A-G is described in ClinVar as [Benign]. Clinvar id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CIDEC	NM_001321142.2	c.*293T>C		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.*293T>C		3_prime_UTR_variant	7/7	1	NM_001321142.2	ENSP00000338642	A1

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

Gnomad4 AFR exome AF: 0.805

Gnomad4 AMR exome AF: 0.685

Gnomad4 ASJ exome AF: 0.788

Gnomad4 EAS exome AF: 0.755

Gnomad4 SAS exome AF: 0.803

Gnomad4 FIN exome AF: 0.759

Gnomad4 NFE exome AF: 0.807

Gnomad4 OTH exome AF: 0.797

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

Gnomad4 AFR AF: 0.799

Gnomad4 AMR AF: 0.723

Gnomad4 ASJ AF: 0.799

Gnomad4 EAS AF: 0.759

Gnomad4 SAS AF: 0.803

Gnomad4 FIN AF: 0.764

Gnomad4 NFE AF: 0.807

Gnomad4 OTH AF: 0.794

Alfa AF: 0.802 Hom.: 65076

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

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 10, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.065
DANN	Benign	0.54

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: rs2479; hg19: chr3-9908525;