4-102872408-T-A

Variant names:

• chr4-102872408-T-A
• rs223331
• NM_001008388.5:c.103+3221T>A

Variant summary

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

The NM_001008388.5(CISD2):​c.103+3221T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 152,038 control chromosomes in the GnomAD database, including 10,693 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 0.37 (10693 hom., cov: 32)
• Consequence: CISD2 NM_001008388.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.215
• Publications: 11 publications found

Genes affected

CISD2 (HGNC:24212): (CDGSH iron sulfur domain 2) The protein encoded by this gene is a zinc finger protein that localizes to the endoplasmic reticulum. The encoded protein binds an iron/sulfur cluster and may be involved in calcium homeostasis. Defects in this gene are a cause of Wolfram syndrome 2. [provided by RefSeq, Mar 2011]

CISD2 Gene-Disease associations (from GenCC):

• Wolfram syndrome

  Inheritance: AR Classification: DEFINITIVE, SUPPORTIVE Submitted by: ClinGen, Orphanet
• Wolfram syndrome 2

  Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Genomics England PanelApp, PanelApp Australia, G2P, Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001008388.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CISD2	NM_001008388.5	MANE Select	c.103+3221T>A		intron	N/A	NP_001008389.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CISD2	ENST00000273986.10	TSL:1 MANE Select	c.103+3221T>A		intron	N/A	ENSP00000273986.4
	CISD2	ENST00000503643.1	TSL:2	c.133+2896T>A		intron	N/A	ENSP00000423716.1
	CISD2	ENST00000895599.1		c.103+3221T>A		intron	N/A	ENSP00000565658.1

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56629 AN: 151920 Hom.: 10685 Cov.: 32

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.373 AC: 56663 AN: 152038 Hom.: 10693 Cov.: 32 AF XY: 0.374 AC XY: 27824 AN XY: 74310

African (AFR) AF: 0.436 AC: 18077 AN: 41442

American (AMR) AF: 0.374 AC: 5718 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 1356 AN: 3472

East Asian (EAS) AF: 0.377 AC: 1952 AN: 5178

South Asian (SAS) AF: 0.382 AC: 1838 AN: 4816

European-Finnish (FIN) AF: 0.372 AC: 3923 AN: 10556

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22657 AN: 67982

Other (OTH) AF: 0.375 AC: 789 AN: 2106

Alfa AF: 0.221 Hom.: 436

Bravo AF: 0.381

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.0
DANN	Benign	0.60
PhyloP100		0.21
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: rs223331; hg19: chr4-103793565;