chr22-30926821-G-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2
The NM_001303256.3(MORC2):c.3081C>T(p.Leu1027=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,613,656 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. L1027L) has been classified as Likely benign.
Frequency
Consequence
NM_001303256.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MORC2 | NM_001303256.3 | c.3081C>T | p.Leu1027= | synonymous_variant | 26/26 | ENST00000397641.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MORC2 | ENST00000397641.8 | c.3081C>T | p.Leu1027= | synonymous_variant | 26/26 | 5 | NM_001303256.3 | P1 | |
MORC2-AS1 | ENST00000441558.1 | n.68-3056G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000921 AC: 14AN: 152070Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000518 AC: 13AN: 251022Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135724
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461468Hom.: 0 Cov.: 30 AF XY: 0.0000151 AC XY: 11AN XY: 727090
GnomAD4 genome ? AF: 0.0000920 AC: 14AN: 152188Hom.: 0 Cov.: 31 AF XY: 0.0000806 AC XY: 6AN XY: 74408
ClinVar
Submissions by phenotype
Charcot-Marie-Tooth disease axonal type 2Z Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 09, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at