18-12274698-T-C

Variant names:

• chr18-12274698-T-C
• rs7230480
• NM_001279.4:c.512+424T>C

Variant summary

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

The NM_001279.4(CIDEA):​c.512+424T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.769 in 152,096 control chromosomes in the GnomAD database, including 45,145 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 0.77 (45145 hom., cov: 32)
• Consequence: CIDEA NM_001279.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.66
• Publications: 10 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.846 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CIDEA	NM_001279.4	c.512+424T>C		intron_variant	Intron 4 of 4	ENST00000320477.10	NP_001270.1
CIDEA	NM_001318383.2	c.614+424T>C		intron_variant	Intron 4 of 4		NP_001305312.1
CIDEA	NR_134607.2	n.1337+424T>C		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CIDEA	ENST00000320477.10	c.512+424T>C		intron_variant	Intron 4 of 4	1	NM_001279.4	ENSP00000320209.8
CIDEA	ENST00000521296.5	n.729+424T>C		intron_variant	Intron 4 of 4	1
CIDEA	ENST00000520620.1	n.525-2425T>C		intron_variant	Intron 3 of 3	3
CIDEA	ENST00000522713.5	n.*711+424T>C		intron_variant	Intron 5 of 5	2		ENSP00000429238.1

Frequencies

GnomAD3 genomes AF: 0.769 AC: 116858 AN: 151978 Hom.: 45119 Cov.: 32

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.767

Gnomad AMR AF: 0.799

Gnomad ASJ AF: 0.839

Gnomad EAS AF: 0.868

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.755

Gnomad OTH AF: 0.769

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

GnomAD4 genome AF: 0.769 AC: 116934 AN: 152096 Hom.: 45145 Cov.: 32 AF XY: 0.765 AC XY: 56852 AN XY: 74340

African (AFR) AF: 0.795 AC: 32962 AN: 41470

American (AMR) AF: 0.799 AC: 12218 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.839 AC: 2906 AN: 3464

East Asian (EAS) AF: 0.867 AC: 4488 AN: 5174

South Asian (SAS) AF: 0.712 AC: 3435 AN: 4822

European-Finnish (FIN) AF: 0.662 AC: 6988 AN: 10554

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.755 AC: 51372 AN: 68010

Other (OTH) AF: 0.769 AC: 1626 AN: 2114

Alfa AF: 0.768 Hom.: 138716

Bravo AF: 0.784

Asia WGS AF: 0.761 AC: 2649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.13
DANN	Benign	0.29
PhyloP100		-2.7
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: rs7230480; hg19: chr18-12274697; COSMIC: COSV57600945; COSMIC: COSV57600945;