Variant rs2879097 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001136498.2(CISD3):c.235C>T(p.Arg79Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 1,551,446 control chromosomes in the GnomAD database, including 39,210 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 ( 2889 hom., cov: 33)

Exomes 𝑓: 0.22 ( 36321 hom. )

Consequence

CISD3
NM_001136498.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.996

Variant links:

Genes affected

CISD3 (HGNC:27578): (CDGSH iron sulfur domain 3) CISD3 is a member of the CDGSH domain-containing family, which may play a role in regulating electron transport and oxidative phosphorylation (Wiley et al., 2007 [PubMed 17376863]).[supplied by OMIM, Apr 2008]

CISD3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CISD3	NM_001136498.2 linkuse as main transcript	c.235C>T	p.Arg79Cys	missense_variant	4/4	ENST00000613478.2	NP_001129970.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
CISD3	ENST00000613478.2 linkuse as main transcript	c.235C>T	p.Arg79Cys	missense_variant	4/4	2	NM_001136498.2	ENSP00000483781	P1
CISD3	ENST00000619858.1 linkuse as main transcript	n.588C>T		non_coding_transcript_exon_variant	3/3	1
CISD3	ENST00000616128.1 linkuse as main transcript	n.364C>T		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes

AF:

0.180

AC:

27331

AN:

152136

Hom.:

2889

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0696

Gnomad AMI

AF:

0.291

Gnomad AMR

AF:

0.270

Gnomad ASJ

AF:

0.228

Gnomad EAS

AF:

0.138

Gnomad SAS

AF:

0.164

Gnomad FIN

AF:

0.146

Gnomad MID

AF:

0.161

Gnomad NFE

AF:

0.232

Gnomad OTH

AF:

0.179

GnomAD3 exomes

AF:

0.212

AC:

32679

AN:

153932

Hom.:

3844

AF XY:

0.208

AC XY:

16959

AN XY:

81694

show subpopulations

Gnomad AFR exome

AF:

0.0653

Gnomad AMR exome

AF:

0.314

Gnomad ASJ exome

AF:

0.233

Gnomad EAS exome

AF:

0.138

Gnomad SAS exome

AF:

0.172

Gnomad FIN exome

AF:

0.145

Gnomad NFE exome

AF:

0.233

Gnomad OTH exome

AF:

0.212

GnomAD4 exome

AF:

0.223

AC:

312346

AN:

1399190

Hom.:

36321

Cov.:

AF XY:

0.222

AC XY:

153162

AN XY:

690118

show subpopulations

Gnomad4 AFR exome

AF:

0.0647

Gnomad4 AMR exome

AF:

0.309

Gnomad4 ASJ exome

AF:

0.232

Gnomad4 EAS exome

AF:

0.117

Gnomad4 SAS exome

AF:

0.168

Gnomad4 FIN exome

AF:

0.155

Gnomad4 NFE exome

AF:

0.236

Gnomad4 OTH exome

AF:

0.209

GnomAD4 genome

AF:

0.180

AC:

27331

AN:

152256

Hom.:

2889

Cov.:

AF XY:

0.175

AC XY:

13058

AN XY:

74440

show subpopulations

Gnomad4 AFR

AF:

0.0695

Gnomad4 AMR

AF:

0.270

Gnomad4 ASJ

AF:

0.228

Gnomad4 EAS

AF:

0.138

Gnomad4 SAS

AF:

0.164

Gnomad4 FIN

AF:

0.146

Gnomad4 NFE

AF:

0.232

Gnomad4 OTH

AF:

0.177

Alfa

AF:

0.222

Hom.:

8061

Bravo

AF:

0.184

TwinsUK

AF:

0.239

AC:

887

ALSPAC

AF:

0.237

AC:

914

ExAC

AF:

0.164

AC:

3963

Asia WGS

AF:

0.127

AC:

443

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.33

BayesDel_addAF

Benign

-0.48

BayesDel_noAF

Benign

-0.31

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.0062

Eigen

Uncertain

0.27

Eigen_PC

Uncertain

0.25

FATHMM_MKL

Benign

0.71

MetaRNN

Benign

0.0014

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.2

MutationTaster

Benign

0.024

PrimateAI

Benign

0.43

Sift4G

Uncertain

0.029

Polyphen

1.0

Vest4

0.13

ClinPred

0.020

GERP RS

3.3

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.44

gMVP

0.54

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.24

Details are displayed if max score is > 0.2

DS_AL_spliceai

0.24

Position offset: -30

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over