rs567254059
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_015374.3(SUN2):c.1275G>A(p.Leu425=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000384 in 1,587,376 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. L425L) has been classified as Likely benign.
Frequency
Consequence
NM_015374.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SUN2 | NM_015374.3 | c.1275G>A | p.Leu425= | synonymous_variant | 12/18 | ENST00000689035.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SUN2 | ENST00000689035.1 | c.1275G>A | p.Leu425= | synonymous_variant | 12/18 | NM_015374.3 | P2 | ||
ENST00000416406.1 | n.165+1181C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000450 AC: 9AN: 199918Hom.: 0 AF XY: 0.0000184 AC XY: 2AN XY: 108792
GnomAD4 exome AF: 0.0000362 AC: 52AN: 1435054Hom.: 0 Cov.: 31 AF XY: 0.0000323 AC XY: 23AN XY: 711470
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152322Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74476
ClinVar
Submissions by phenotype
Emery-Dreifuss muscular dystrophy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 03, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at