chr4-102869094-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001008388.5(CISD2):c.10G>C(p.Glu4Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,458,806 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. E4E) has been classified as Likely benign.
Frequency
Consequence
NM_001008388.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CISD2 | NM_001008388.5 | c.10G>C | p.Glu4Gln | missense_variant | 1/3 | ENST00000273986.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CISD2 | ENST00000273986.10 | c.10G>C | p.Glu4Gln | missense_variant | 1/3 | 1 | NM_001008388.5 | P1 | |
CISD2 | ENST00000574446.1 | c.10G>C | p.Glu4Gln | missense_variant, NMD_transcript_variant | 1/4 | 5 | |||
CISD2 | ENST00000646632.1 | c.10G>C | p.Glu4Gln | missense_variant, NMD_transcript_variant | 1/4 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000820 AC: 2AN: 243804Hom.: 0 AF XY: 0.0000151 AC XY: 2AN XY: 132216
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1458806Hom.: 0 Cov.: 33 AF XY: 0.00000551 AC XY: 4AN XY: 725380
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 20, 2021 | The c.10G>C (p.E4Q) alteration is located in exon 1 (coding exon 1) of the CISD2 gene. This alteration results from a G to C substitution at nucleotide position 10, causing the glutamic acid (E) at amino acid position 4 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at