5-6599379-TG-T
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_017755.6(NSUN2):c.*546del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0396 in 152,842 control chromosomes in the GnomAD database, including 147 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.040 ( 147 hom., cov: 32)
Exomes 𝑓: 0.040 ( 0 hom. )
Consequence
NSUN2
NM_017755.6 3_prime_UTR
NM_017755.6 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.834
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 -10 ACMG points.
BP6
Variant 5-6599379-TG-T is Benign according to our data. Variant chr5-6599379-TG-T is described in ClinVar as [Likely_benign]. Clinvar id is 354040.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0558 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NSUN2 | NM_017755.6 | c.*546del | 3_prime_UTR_variant | 19/19 | ENST00000264670.11 | ||
NSUN2 | NM_001193455.2 | c.*546del | 3_prime_UTR_variant | 18/18 | |||
NSUN2 | NR_037947.2 | n.2830del | non_coding_transcript_exon_variant | 18/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NSUN2 | ENST00000264670.11 | c.*546del | 3_prime_UTR_variant | 19/19 | 1 | NM_017755.6 | P2 | ||
LINC01018 | ENST00000661215.1 | n.757-739del | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0396 AC: 6021AN: 152148Hom.: 147 Cov.: 32
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GnomAD4 exome AF: 0.0399 AC: 23AN: 576Hom.: 0 Cov.: 0 AF XY: 0.0460 AC XY: 16AN XY: 348
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GnomAD4 genome AF: 0.0395 AC: 6022AN: 152266Hom.: 147 Cov.: 32 AF XY: 0.0385 AC XY: 2868AN XY: 74452
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Intellectual Disability, Recessive Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at