chr15-34753091-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020660.3(GJD2):c.353G>A(p.Arg118Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000372 in 1,613,988 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020660.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GJD2 | NM_020660.3 | c.353G>A | p.Arg118Lys | missense_variant | Exon 2 of 2 | ENST00000290374.5 | NP_065711.1 | |
GJD2 | XM_017022438.2 | c.200G>A | p.Arg67Lys | missense_variant | Exon 2 of 2 | XP_016877927.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152132Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000956 AC: 24AN: 250966Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135764
GnomAD4 exome AF: 0.0000363 AC: 53AN: 1461856Hom.: 0 Cov.: 41 AF XY: 0.0000358 AC XY: 26AN XY: 727226
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152132Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74308
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.353G>A (p.R118K) alteration is located in exon 2 (coding exon 2) of the GJD2 gene. This alteration results from a G to A substitution at nucleotide position 353, causing the arginine (R) at amino acid position 118 to be replaced by a lysine (K). 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