NM_001321142.2:c.181T>C

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001321142.2(CIDEC):c.181T>C(p.Tyr61His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0102 in 1,553,410 control chromosomes in the GnomAD database, including 378 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.018 ( 53 hom., cov: 32)

Exomes 𝑓: 0.0094 ( 325 hom. )

Consequence

CIDEC
NM_001321142.2 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.0900

Publications

9 publications found

Variant links:

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

CIDEC links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (MetaRNN=0.009500384).

BP6

Variant 3-9877092-A-G is Benign according to our data. Variant chr3-9877092-A-G is described in ClinVar as Benign. ClinVar VariationId is 128771.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0743 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

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
CIDEC	NM_001321142.2	MANE Select	c.181T>C	p.Tyr61His	missense	Exon 4 of 7	NP_001308071.1	Q96AQ7-1
CIDEC	NM_001199623.2		c.220T>C	p.Tyr74His	missense	Exon 3 of 6	NP_001186552.1	A0A0A0MRY9
CIDEC	NM_001199551.2		c.181T>C	p.Tyr61His	missense	Exon 3 of 7	NP_001186480.1	Q96AQ7-4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
CIDEC	ENST00000336832.7	TSL:1 MANE Select	c.181T>C	p.Tyr61His	missense	Exon 4 of 7	ENSP00000338642.2	Q96AQ7-1
CIDEC	ENST00000383817.5	TSL:1	c.220T>C	p.Tyr74His	missense	Exon 3 of 6	ENSP00000373328.2	A0A0A0MRY9
CIDEC	ENST00000443115.1	TSL:1	c.181T>C	p.Tyr61His	missense	Exon 2 of 3	ENSP00000411356.1	A0A0C4DG75

Frequencies

GnomAD3 genomes

AF:

0.0175

AC:

2657

AN:

152180

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0354

Gnomad AMI

AF:

0.00548

Gnomad AMR

AF:

0.0204

Gnomad ASJ

AF:

0.0109

Gnomad EAS

AF:

0.00731

Gnomad SAS

AF:

0.0810

Gnomad FIN

AF:

0.00697

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00423

Gnomad OTH

AF:

0.0182

GnomAD2 exomes

AF:

0.0184

AC:

2935

AN:

159410

AF XY:

0.0206

show subpopulations

Gnomad AFR exome

AF:

0.0338

Gnomad AMR exome

AF:

0.0171

Gnomad ASJ exome

AF:

0.0107

Gnomad EAS exome

AF:

0.00571

Gnomad FIN exome

AF:

0.00645

Gnomad NFE exome

AF:

0.00459

Gnomad OTH exome

AF:

0.0139

GnomAD4 exome

AF:

0.00943

AC:

13211

AN:

1401112

Hom.:

325

Cov.:

AF XY:

0.0110

AC XY:

7627

AN XY:

691208

show subpopulations

African (AFR)

AF:

0.0371

AC:

1179

AN:

31750

American (AMR)

AF:

0.0163

AC:

582

AN:

35794

Ashkenazi Jewish (ASJ)

AF:

0.0109

AC:

274

AN:

25190

East Asian (EAS)

AF:

0.00249

AC:

AN:

36114

South Asian (SAS)

AF:

0.0695

AC:

5516

AN:

79316

European-Finnish (FIN)

AF:

0.00607

AC:

300

AN:

49402

Middle Eastern (MID)

AF:

0.0236

AC:

134

AN:

5666

European-Non Finnish (NFE)

AF:

0.00398

AC:

4295

AN:

1079808

Other (OTH)

AF:

0.0145

AC:

841

AN:

58072

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

809

1618

2427

3236

4045

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

230

460

690

920

1150

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0175

AC:

2667

AN:

152298

Hom.:

Cov.:

AF XY:

0.0189

AC XY:

1410

AN XY:

74470

show subpopulations

African (AFR)

AF:

0.0355

AC:

1477

AN:

41582

American (AMR)

AF:

0.0204

AC:

312

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.0109

AC:

AN:

3472

East Asian (EAS)

AF:

0.00733

AC:

AN:

5184

South Asian (SAS)

AF:

0.0809

AC:

390

AN:

4822

European-Finnish (FIN)

AF:

0.00697

AC:

AN:

10618

Middle Eastern (MID)

AF:

0.0102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00423

AC:

288

AN:

68018

Other (OTH)

AF:

0.0199

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

134

268

401

535

669

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

160

200

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00927

Hom.:

Bravo

AF:

0.0169

TwinsUK

AF:

0.00378

AC:

ALSPAC

AF:

0.00441

AC:

ESP6500AA

AF:

0.0314

AC:

136

ESP6500EA

AF:

0.00236

AC:

ExAC

AF:

0.0109

AC:

1137

Asia WGS

AF:

0.0460

AC:

160

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

CIDEC-related disorder (1)

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.056

BayesDel_addAF

Benign

-0.73

BayesDel_noAF

Benign

-0.77

CADD

Benign

1.6

(source)

DANN

Benign

0.26

Eigen

Benign

-1.3

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.013

LIST_S2

Benign

0.27

MetaRNN

Benign

0.0095

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-1.7

PhyloP100

0.090

PrimateAI

Benign

0.28

PROVEAN

Benign

0.88

REVEL

Benign

0.045

Sift

Benign

0.59

Sift4G

Benign

0.61

Polyphen

0.0

Vest4

0.061

MPC

0.016

ClinPred

0.00029

GERP RS

1.3

Varity_R

0.019

gMVP

0.20

Mutation Taster

=99/1

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over