2-69829930-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_178439.5(GMCL1):c.38G>A(p.Arg13Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000138 in 1,452,840 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_178439.5 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 |
---|---|---|---|---|---|---|---|
GMCL1 | NM_178439.5 | c.38G>A | p.Arg13Lys | missense_variant | 1/14 | ENST00000282570.4 | |
GMCL1 | XM_011533033.3 | c.38G>A | p.Arg13Lys | missense_variant | 1/13 | ||
GMCL1 | XR_007079574.1 | n.271G>A | non_coding_transcript_exon_variant | 1/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GMCL1 | ENST00000282570.4 | c.38G>A | p.Arg13Lys | missense_variant | 1/14 | 1 | NM_178439.5 | P1 | |
GMCL1 | ENST00000468386.2 | n.245G>A | non_coding_transcript_exon_variant | 1/4 | 5 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000133 AC: 3AN: 224808Hom.: 0 AF XY: 0.00000812 AC XY: 1AN XY: 123186
GnomAD4 exome AF: 0.0000138 AC: 20AN: 1452840Hom.: 0 Cov.: 31 AF XY: 0.0000125 AC XY: 9AN XY: 721886
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 03, 2023 | The c.38G>A (p.R13K) alteration is located in exon 1 (coding exon 1) of the GMCL1 gene. This alteration results from a G to A substitution at nucleotide position 38, causing the arginine (R) at amino acid position 13 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