3-9866972-C-T

Variant names:

• chr3-9866972-C-T
• rs28575453
• NM_001321142.2:c.*162G>A

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.*162G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0526 in 822,126 control chromosomes in the GnomAD database, including 1,444 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.045 (217 hom., cov: 33)
  • Exomes 𝑓: 0.054 (1227 hom.)
• Consequence: CIDEC NM_001321142.2 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.282

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 3-9866972-C-T is Benign according to our data. Variant chr3-9866972-C-T is described in ClinVar as [Benign]. Clinvar id is 1281717.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0642 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CIDEC	NM_001321142.2	c.*162G>A		3_prime_UTR_variant	Exon 7 of 7	ENST00000336832.7	NP_001308071.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CIDEC	ENST00000336832	c.*162G>A		3_prime_UTR_variant	Exon 7 of 7	1	NM_001321142.2	ENSP00000338642.2

Frequencies

GnomAD3 genomes AF: 0.0446 AC: 6781 AN: 152210 Hom.: 217 Cov.: 33

Gnomad AFR AF: 0.0132

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.0474

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0267

Gnomad FIN AF: 0.0202

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0658

Gnomad OTH AF: 0.0559

GnomAD4 exome AF: 0.0545 AC: 36478 AN: 669798 Hom.: 1227 Cov.: 9 AF XY: 0.0544 AC XY: 19457 AN XY: 357828

Gnomad4 AFR exome AF: 0.0125 AC: 227 AN: 18174

Gnomad4 AMR exome AF: 0.0370 AC: 1405 AN: 37960

Gnomad4 ASJ exome AF: 0.123 AC: 2513 AN: 20446

Gnomad4 EAS exome AF: 0.000731 AC: 25 AN: 34198

Gnomad4 SAS exome AF: 0.0341 AC: 2298 AN: 67338

Gnomad4 FIN exome AF: 0.0248 AC: 1087 AN: 43870

Gnomad4 NFE exome AF: 0.0648 AC: 26640 AN: 410826

Gnomad4 Remaining exome AF: 0.0605 AC: 2077 AN: 34330

GnomAD4 genome AF: 0.0445 AC: 6782 AN: 152328 Hom.: 217 Cov.: 33 AF XY: 0.0416 AC XY: 3098 AN XY: 74488

Gnomad4 AFR AF: 0.0131 AC: 0.0131301 AN: 0.0131301

Gnomad4 AMR AF: 0.0473 AC: 0.0473388 AN: 0.0473388

Gnomad4 ASJ AF: 0.129 AC: 0.129395 AN: 0.129395

Gnomad4 EAS AF: 0.00116 AC: 0.00115607 AN: 0.00115607

Gnomad4 SAS AF: 0.0269 AC: 0.0269486 AN: 0.0269486

Gnomad4 FIN AF: 0.0202 AC: 0.0202372 AN: 0.0202372

Gnomad4 NFE AF: 0.0658 AC: 0.0658042 AN: 0.0658042

Gnomad4 OTH AF: 0.0553 AC: 0.055293 AN: 0.055293

Alfa AF: 0.0506 Hom.: 24

Bravo AF: 0.0455

Asia WGS AF: 0.0200 AC: 71 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Jun 18, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.1
DANN	Benign	0.75
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs28575453; hg19: chr3-9908656;