chr1-84939555-T-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_153259.4(MCOLN2):āc.1108A>Cā(p.Lys370Gln) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00447 in 1,613,912 control chromosomes in the GnomAD database, including 309 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_153259.4 missense, splice_region
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.1108A>C | p.Lys370Gln | missense_variant, splice_region_variant | 9/14 | ENST00000370608.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MCOLN2 | ENST00000370608.8 | c.1108A>C | p.Lys370Gln | missense_variant, splice_region_variant | 9/14 | 1 | NM_153259.4 | ||
MCOLN2 | ENST00000531325.5 | n.1349A>C | splice_region_variant, non_coding_transcript_exon_variant | 9/12 | 1 | ||||
MCOLN2 | ENST00000284027.5 | c.1024A>C | p.Lys342Gln | missense_variant, splice_region_variant | 9/14 | 5 | P1 | ||
MCOLN2 | ENST00000463065.5 | c.*45-1473A>C | intron_variant, NMD_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0237 AC: 3607AN: 152150Hom.: 164 Cov.: 32
GnomAD3 exomes AF: 0.00630 AC: 1581AN: 250984Hom.: 61 AF XY: 0.00448 AC XY: 607AN XY: 135632
GnomAD4 exome AF: 0.00246 AC: 3599AN: 1461644Hom.: 144 Cov.: 31 AF XY: 0.00200 AC XY: 1453AN XY: 727134
GnomAD4 genome AF: 0.0238 AC: 3617AN: 152268Hom.: 165 Cov.: 32 AF XY: 0.0226 AC XY: 1684AN XY: 74476
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 03, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at