rs137925849
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_015374.3(SUN2):c.467G>A(p.Arg156Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00022 in 1,613,840 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_015374.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SUN2 | NM_015374.3 | c.467G>A | p.Arg156Gln | missense_variant | 5/18 | ENST00000689035.1 | NP_056189.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SUN2 | ENST00000689035.1 | c.467G>A | p.Arg156Gln | missense_variant | 5/18 | NM_015374.3 | ENSP00000508608 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00115 AC: 175AN: 152216Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000323 AC: 81AN: 250934Hom.: 0 AF XY: 0.000258 AC XY: 35AN XY: 135804
GnomAD4 exome AF: 0.000122 AC: 179AN: 1461506Hom.: 0 Cov.: 32 AF XY: 0.000110 AC XY: 80AN XY: 727052
GnomAD4 genome AF: 0.00116 AC: 176AN: 152334Hom.: 0 Cov.: 33 AF XY: 0.00121 AC XY: 90AN XY: 74486
ClinVar
Submissions by phenotype
Emery-Dreifuss muscular dystrophy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 22, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at