rs544208812
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001130965.3(SUN1):c.1025C>A(p.Thr342Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,613,694 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T342A) has been classified as Uncertain significance.
Frequency
Consequence
NM_001130965.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SUN1 | NM_001130965.3 | c.1025C>A | p.Thr342Lys | missense_variant | 9/19 | ENST00000401592.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SUN1 | ENST00000401592.6 | c.1025C>A | p.Thr342Lys | missense_variant | 9/19 | 1 | NM_001130965.3 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152194Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000803 AC: 2AN: 249196Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135228
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461382Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726990
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152312Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74476
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at