rs150472251
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_017755.6(NSUN2):c.2280G>C(p.Pro760=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000208 in 1,613,710 control chromosomes in the GnomAD database, including 6 homozygotes. 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. P760P) has been classified as Likely benign.
Frequency
Consequence
NM_017755.6 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NSUN2 | NM_017755.6 | c.2280G>C | p.Pro760= | synonymous_variant | 19/19 | ENST00000264670.11 | |
NSUN2 | NM_001193455.2 | c.2175G>C | p.Pro725= | synonymous_variant | 18/18 | ||
NSUN2 | NR_037947.2 | n.2260G>C | non_coding_transcript_exon_variant | 18/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NSUN2 | ENST00000264670.11 | c.2280G>C | p.Pro760= | synonymous_variant | 19/19 | 1 | NM_017755.6 | P2 | |
LINC01018 | ENST00000661215.1 | n.757-171C>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.000105 AC: 16AN: 152250Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000474 AC: 119AN: 251246Hom.: 4 AF XY: 0.000663 AC XY: 90AN XY: 135782
GnomAD4 exome AF: 0.000218 AC: 319AN: 1461342Hom.: 6 Cov.: 31 AF XY: 0.000314 AC XY: 228AN XY: 726954
GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152368Hom.: 0 Cov.: 33 AF XY: 0.000201 AC XY: 15AN XY: 74518
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jan 04, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at