chr1-84939570-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_153259.4(MCOLN2):c.1093A>G(p.Met365Val) variant causes a missense change. The variant allele was found at a frequency of 0.00509 in 1,613,904 control chromosomes in the GnomAD database, including 379 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_153259.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MCOLN2 | NM_153259.4 | c.1093A>G | p.Met365Val | missense_variant | 9/14 | ENST00000370608.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MCOLN2 | ENST00000370608.8 | c.1093A>G | p.Met365Val | missense_variant | 9/14 | 1 | NM_153259.4 | ||
MCOLN2 | ENST00000531325.5 | n.1334A>G | non_coding_transcript_exon_variant | 9/12 | 1 | ||||
MCOLN2 | ENST00000284027.5 | c.1009A>G | p.Met337Val | missense_variant | 9/14 | 5 | P1 | ||
MCOLN2 | ENST00000463065.5 | c.*45-1488A>G | intron_variant, NMD_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0271 AC: 4128AN: 152136Hom.: 216 Cov.: 32
GnomAD3 exomes AF: 0.00682 AC: 1713AN: 251004Hom.: 83 AF XY: 0.00511 AC XY: 693AN XY: 135660
GnomAD4 exome AF: 0.00279 AC: 4079AN: 1461650Hom.: 164 Cov.: 31 AF XY: 0.00243 AC XY: 1770AN XY: 727126
GnomAD4 genome ? AF: 0.0271 AC: 4132AN: 152254Hom.: 215 Cov.: 32 AF XY: 0.0257 AC XY: 1910AN XY: 74462
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 18, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at