rs8092502

Variant names:

• chr18-12263374-T-C
• rs8092502
• NM_001279.4:c.183+405T>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.183+405T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,060 control chromosomes in the GnomAD database, including 3,752 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 0.17 (3752 hom., cov: 32)
• Consequence: CIDEA NM_001279.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 6 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CIDEA	NM_001279.4	c.183+405T>C		intron_variant	Intron 2 of 4	ENST00000320477.10	NP_001270.1
CIDEA	NM_001318383.2	c.285+405T>C		intron_variant	Intron 2 of 4		NP_001305312.1
CIDEA	NR_134607.2	n.742-226T>C		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CIDEA	ENST00000320477.10	c.183+405T>C		intron_variant	Intron 2 of 4	1	NM_001279.4	ENSP00000320209.8
CIDEA	ENST00000521296.5	n.400+405T>C		intron_variant	Intron 2 of 4	1
CIDEA	ENST00000520620.1	n.377+405T>C		intron_variant	Intron 2 of 3	3
CIDEA	ENST00000522713.5	n.*116-226T>C		intron_variant	Intron 2 of 5	2		ENSP00000429238.1

Frequencies

GnomAD3 genomes AF: 0.171 AC: 26006 AN: 151942 Hom.: 3736 Cov.: 32

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.0784

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.0533

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0587

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.171 AC: 26063 AN: 152060 Hom.: 3752 Cov.: 32 AF XY: 0.171 AC XY: 12709 AN XY: 74336

African (AFR) AF: 0.382 AC: 15814 AN: 41442

American (AMR) AF: 0.232 AC: 3542 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0784 AC: 272 AN: 3470

East Asian (EAS) AF: 0.158 AC: 819 AN: 5168

South Asian (SAS) AF: 0.127 AC: 612 AN: 4804

European-Finnish (FIN) AF: 0.0533 AC: 565 AN: 10594

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0587 AC: 3992 AN: 67998

Other (OTH) AF: 0.152 AC: 320 AN: 2110

Alfa AF: 0.0968 Hom.: 4704

Bravo AF: 0.195

Asia WGS AF: 0.152 AC: 529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.2
DANN	Benign	0.68
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: rs8092502; hg19: chr18-12263373;