18-2656249-G-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BS1BS2
The NM_015295.3(SMCHD1):c.174G>T(p.Ala58=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000255 in 1,492,990 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. A58A) has been classified as Benign.
Frequency
Consequence
NM_015295.3 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 |
---|---|---|---|---|---|---|---|
SMCHD1 | NM_015295.3 | c.174G>T | p.Ala58= | synonymous_variant | 1/48 | ENST00000320876.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMCHD1 | ENST00000320876.11 | c.174G>T | p.Ala58= | synonymous_variant | 1/48 | 5 | NM_015295.3 | P2 | |
SMCHD1 | ENST00000688342.1 | c.174G>T | p.Ala58= | synonymous_variant | 1/47 | A2 | |||
SMCHD1 | ENST00000684915.1 | n.331G>T | non_coding_transcript_exon_variant | 1/14 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152100Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000474 AC: 7AN: 147528Hom.: 0 AF XY: 0.0000479 AC XY: 4AN XY: 83462
GnomAD4 exome AF: 0.0000261 AC: 35AN: 1340890Hom.: 0 Cov.: 46 AF XY: 0.0000437 AC XY: 29AN XY: 664058
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152100Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74284
ClinVar
Submissions by phenotype
Facioscapulohumeral muscular dystrophy 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 23, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at