1-84940883-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_153259.4(MCOLN2):c.956G>A(p.Arg319Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00000684 in 1,608,876 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 (★).
Frequency
Consequence
NM_153259.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MCOLN2 | ENST00000370608.8 | c.956G>A | p.Arg319Gln | missense_variant | Exon 8 of 14 | 1 | NM_153259.4 | ENSP00000359640.3 | ||
MCOLN2 | ENST00000531325.5 | n.1197G>A | non_coding_transcript_exon_variant | Exon 8 of 12 | 1 | |||||
MCOLN2 | ENST00000284027.5 | c.872G>A | p.Arg291Gln | missense_variant | Exon 8 of 14 | 5 | ENSP00000284027.5 | |||
MCOLN2 | ENST00000463065.5 | n.*45-2801G>A | intron_variant | Intron 7 of 11 | 2 | ENSP00000436299.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152114Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000807 AC: 2AN: 247900Hom.: 0 AF XY: 0.00000746 AC XY: 1AN XY: 133968
GnomAD4 exome AF: 0.00000686 AC: 10AN: 1456762Hom.: 0 Cov.: 29 AF XY: 0.00000690 AC XY: 5AN XY: 724872
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152114Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74300
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.956G>A (p.R319Q) alteration is located in exon 8 (coding exon 8) of the MCOLN2 gene. This alteration results from a G to A substitution at nucleotide position 956, causing the arginine (R) at amino acid position 319 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