rs12962340

chr18-12272924-T-Achr18-12272924-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CIDEA	NM_001279.4	c.331-1169T>A		intron_variant		ENST00000320477.10
CIDEA	NM_001318383.2	c.433-1169T>A		intron_variant
CIDEA	NR_134607.2	n.1156-1169T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CIDEA	ENST00000320477.10	c.331-1169T>A		intron_variant		1	NM_001279.4	P1
CIDEA	ENST00000521296.5	n.548-1169T>A		intron_variant, non_coding_transcript_variant		1
CIDEA	ENST00000522713.5	c.*530-1169T>A		intron_variant, NMD_transcript_variant		2
CIDEA	ENST00000520620.1	n.525-4199T>A		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.0511

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.280

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.263

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.192

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	2.8
Dann	Benign	0.78

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: rs12962340; hg19: chr18-12272923;