rs149276590
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM2BP4_StrongBP6_Very_StrongBS1
The NM_017755.6(NSUN2):c.537+8A>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000373 in 1,592,304 control chromosomes in the GnomAD database, including 1 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 Likely benign (★★).
Frequency
Consequence
NM_017755.6 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NSUN2 | NM_017755.6 | c.537+8A>G | splice_region_variant, intron_variant | ENST00000264670.11 | NP_060225.4 | |||
NSUN2 | NM_001193455.2 | c.432+8A>G | splice_region_variant, intron_variant | NP_001180384.1 | ||||
NSUN2 | NR_037947.2 | n.602+8A>G | splice_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NSUN2 | ENST00000264670.11 | c.537+8A>G | splice_region_variant, intron_variant | 1 | NM_017755.6 | ENSP00000264670.6 | ||||
NSUN2 | ENST00000506139.5 | c.432+8A>G | splice_region_variant, intron_variant | 2 | ENSP00000420957.1 | |||||
NSUN2 | ENST00000504374.5 | n.537+8A>G | splice_region_variant, intron_variant | 2 | ENSP00000421783.1 | |||||
NSUN2 | ENST00000505264.1 | n.147+8A>G | splice_region_variant, intron_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.00181 AC: 275AN: 151670Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.000450 AC: 105AN: 233114Hom.: 1 AF XY: 0.000372 AC XY: 47AN XY: 126212
GnomAD4 exome AF: 0.000222 AC: 320AN: 1440516Hom.: 1 Cov.: 31 AF XY: 0.000187 AC XY: 134AN XY: 716204
GnomAD4 genome AF: 0.00181 AC: 274AN: 151788Hom.: 0 Cov.: 30 AF XY: 0.00186 AC XY: 138AN XY: 74176
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jan 19, 2017 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 22, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at