2-96761033-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_020184.4(CNNM4):c.34G>T(p.Gly12Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000247 in 1,215,784 control chromosomes in the GnomAD database, with no homozygous occurrence. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G12R) has been classified as Uncertain significance.
Frequency
Consequence
NM_020184.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CNNM4 | NM_020184.4 | c.34G>T | p.Gly12Cys | missense_variant | 1/7 | ENST00000377075.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CNNM4 | ENST00000377075.3 | c.34G>T | p.Gly12Cys | missense_variant | 1/7 | 1 | NM_020184.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000668 AC: 1AN: 149752Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.00000188 AC: 2AN: 1066032Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 503418
GnomAD4 genome AF: 0.00000668 AC: 1AN: 149752Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 73014
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 15, 2023 | The c.34G>T (p.G12C) alteration is located in exon 1 (coding exon 1) of the CNNM4 gene. This alteration results from a G to T substitution at nucleotide position 34, causing the glycine (G) at amino acid position 12 to be replaced by a cysteine (C). 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