7-2572268-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152558.5(IQCE):āc.336C>Gā(p.Asp112Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000316 in 1,614,110 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_152558.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IQCE | NM_152558.5 | c.336C>G | p.Asp112Glu | missense_variant | 5/22 | ENST00000402050.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IQCE | ENST00000402050.7 | c.336C>G | p.Asp112Glu | missense_variant | 5/22 | 1 | NM_152558.5 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152272Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000176 AC: 44AN: 249504Hom.: 0 AF XY: 0.0000813 AC XY: 11AN XY: 135374
GnomAD4 exome AF: 0.0000335 AC: 49AN: 1461838Hom.: 0 Cov.: 33 AF XY: 0.0000220 AC XY: 16AN XY: 727220
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152272Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74396
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 31, 2024 | The c.336C>G (p.D112E) alteration is located in exon 5 (coding exon 5) of the IQCE gene. This alteration results from a C to G substitution at nucleotide position 336, causing the aspartic acid (D) at amino acid position 112 to be replaced by a glutamic acid (E). 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