rs8092502

chr18-12263374-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.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

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=-0.91).
• 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/exons	MANE	UniProt
CIDEA	NM_001279.4	c.183+405T>C		intron_variant		ENST00000320477.10
CIDEA	NM_001318383.2	c.285+405T>C		intron_variant
CIDEA	NR_134607.2	n.742-226T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CIDEA	ENST00000320477.10	c.183+405T>C		intron_variant		1	NM_001279.4	P1
CIDEA	ENST00000521296.5	n.400+405T>C		intron_variant, non_coding_transcript_variant		1
CIDEA	ENST00000522713.5	c.*116-226T>C		intron_variant, NMD_transcript_variant		2
CIDEA	ENST00000520620.1	n.377+405T>C		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.0784

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.0533

Gnomad4 NFE AF: 0.0587

Gnomad4 OTH AF: 0.152

Alfa AF: 0.0779 Hom.: 1125

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

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: rs8092502; hg19: chr18-12263373;