chr18-12272924-T-A

Variant names:

• chr18-12272924-T-A
• rs12962340
• NM_001279.4:c.331-1169T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001279.4(CIDEA):​c.331-1169T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,166 control chromosomes in the GnomAD database, including 3,016 homozygotes. 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: 𝑓 0.18 (3016 hom., cov: 32)
• Consequence: CIDEA NM_001279.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 5 publications found

Genes affected

CIDEA (HGNC:1976): (cell death inducing DFFA like effector a) This gene encodes the homolog of the mouse protein Cidea that has been shown to activate apoptosis. This activation of apoptosis is inhibited by the DNA fragmentation factor DFF45 but not by caspase inhibitors. Mice that lack functional Cidea have higher metabolic rates, higher lipolysis in brown adipose tissue and higher core body temperatures when subjected to cold. These mice are also resistant to diet-induced obesity and diabetes. This suggests that in mice this gene product plays a role in thermogenesis and lipolysis. Alternatively spliced transcripts have been identified. [provided by RefSeq, Aug 2010]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001279.4. 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
	CIDEA	NM_001279.4	MANE Select	c.331-1169T>A		intron	N/A	NP_001270.1
	CIDEA	NM_001318383.2		c.433-1169T>A		intron	N/A	NP_001305312.1
	CIDEA	NR_134607.2		n.1156-1169T>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CIDEA	ENST00000320477.10	TSL:1 MANE Select	c.331-1169T>A		intron	N/A	ENSP00000320209.8
	CIDEA	ENST00000521296.5	TSL:1	n.548-1169T>A		intron	N/A
	CIDEA	ENST00000520620.1	TSL:3	n.525-4199T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27513 AN: 152048 Hom.: 3016 Cov.: 32

Gnomad AFR AF: 0.0513

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.194

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.181 AC: 27514 AN: 152166 Hom.: 3016 Cov.: 32 AF XY: 0.185 AC XY: 13742 AN XY: 74372

African (AFR) AF: 0.0511 AC: 2125 AN: 41550

American (AMR) AF: 0.242 AC: 3703 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 972 AN: 3472

East Asian (EAS) AF: 0.236 AC: 1221 AN: 5164

South Asian (SAS) AF: 0.169 AC: 816 AN: 4824

European-Finnish (FIN) AF: 0.263 AC: 2778 AN: 10566

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15207 AN: 67978

Other (OTH) AF: 0.192 AC: 405 AN: 2110

Alfa AF: 0.111 Hom.: 167

Bravo AF: 0.174

Asia WGS AF: 0.192 AC: 665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.8
DANN	Benign	0.78
PhyloP100		0.31
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: rs12962340; hg19: chr18-12272923;