rs138079219
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_015374.3(SUN2):c.1356C>T(p.Asp452=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00179 in 1,573,900 control chromosomes in the GnomAD database, including 49 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_015374.3 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SUN2 | NM_015374.3 | c.1356C>T | p.Asp452= | splice_region_variant, synonymous_variant | 12/18 | ENST00000689035.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SUN2 | ENST00000689035.1 | c.1356C>T | p.Asp452= | splice_region_variant, synonymous_variant | 12/18 | NM_015374.3 | P2 | ||
ENST00000416406.1 | n.165+1100G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00948 AC: 1442AN: 152168Hom.: 27 Cov.: 32
GnomAD3 exomes AF: 0.00246 AC: 522AN: 211870Hom.: 9 AF XY: 0.00186 AC XY: 216AN XY: 115938
GnomAD4 exome AF: 0.000959 AC: 1363AN: 1421614Hom.: 22 Cov.: 31 AF XY: 0.000861 AC XY: 605AN XY: 702760
GnomAD4 genome ? AF: 0.00950 AC: 1447AN: 152286Hom.: 27 Cov.: 32 AF XY: 0.00924 AC XY: 688AN XY: 74454
ClinVar
Submissions by phenotype
Emery-Dreifuss muscular dystrophy Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at