rs186098993
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 2P and 17B. PM2BP4_StrongBP6_Very_StrongBP7BS1
The NM_017755.6(NSUN2):c.561T>C(p.Pro187Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 1,614,086 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.000098 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000012 ( 0 hom. )
Consequence
NSUN2
NM_017755.6 synonymous
NM_017755.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0400
Genes affected
NSUN2 (HGNC:25994): (NOP2/Sun RNA methyltransferase 2) This gene encodes a methyltransferase that catalyzes the methylation of cytosine to 5-methylcytosine (m5C) at position 34 of intron-containing tRNA(Leu)(CAA) precursors. This modification is necessary to stabilize the anticodon-codon pairing and correctly translate the mRNA. Alternatively spliced transcript variants encoding different isoforms have been noted for this gene.[provided by RefSeq, Mar 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.55).
BP6
Variant 5-6622077-A-G is Benign according to our data. Variant chr5-6622077-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 436086.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-0.04 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0000984 (15/152398) while in subpopulation AFR AF= 0.000337 (14/41600). AF 95% confidence interval is 0.000203. There are 0 homozygotes in gnomad4. There are 8 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NSUN2 | NM_017755.6 | c.561T>C | p.Pro187Pro | synonymous_variant | Exon 6 of 19 | ENST00000264670.11 | NP_060225.4 | |
NSUN2 | NM_001193455.2 | c.456T>C | p.Pro152Pro | synonymous_variant | Exon 5 of 18 | NP_001180384.1 | ||
NSUN2 | NR_037947.2 | n.602+1137T>C | intron_variant | Intron 5 of 17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NSUN2 | ENST00000264670.11 | c.561T>C | p.Pro187Pro | synonymous_variant | Exon 6 of 19 | 1 | NM_017755.6 | ENSP00000264670.6 | ||
NSUN2 | ENST00000506139.5 | c.456T>C | p.Pro152Pro | synonymous_variant | Exon 5 of 18 | 2 | ENSP00000420957.1 | |||
NSUN2 | ENST00000504374.5 | n.537+1137T>C | intron_variant | Intron 5 of 17 | 2 | ENSP00000421783.1 | ||||
NSUN2 | ENST00000505264.1 | n.148-333T>C | intron_variant | Intron 2 of 3 | 4 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152280Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251410Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135866
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GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461688Hom.: 0 Cov.: 30 AF XY: 0.0000124 AC XY: 9AN XY: 727174
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GnomAD4 genome AF: 0.0000984 AC: 15AN: 152398Hom.: 0 Cov.: 32 AF XY: 0.000107 AC XY: 8AN XY: 74532
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
May 26, 2017
Genetic Services Laboratory, University of Chicago
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
not provided Benign:1
Feb 26, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at