rs8192120

Positions:

• chr5-6632207-C-A
• chr5-6632207-C-G
• chr5-6632207-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_017755.6(NSUN2):​c.255-230G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 151,462 control chromosomes in the GnomAD database, including 15,964 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.45 (15964 hom., cov: 32)
• Consequence: NSUN2 NM_017755.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0230

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BP6: Variant 5-6632207-C-A is Benign according to our data. Variant chr5-6632207-C-A is described in ClinVar as [Benign]. Clinvar id is 1230653.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NSUN2	NM_017755.6	c.255-230G>T		intron_variant		ENST00000264670.11
NSUN2	NM_001193455.2	c.254+392G>T		intron_variant
NSUN2	NR_037947.2	n.320-230G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NSUN2	ENST00000264670.11	c.255-230G>T		intron_variant		1	NM_017755.6	P2
NSUN2	ENST00000506139.5	c.254+392G>T		intron_variant		2		A2
NSUN2	ENST00000504374.5	c.255-230G>T		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67587 AN: 151344 Hom.: 15960 Cov.: 32

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.406

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.446 AC: 67623 AN: 151462 Hom.: 15964 Cov.: 32 AF XY: 0.452 AC XY: 33419 AN XY: 73946

Gnomad4 AFR AF: 0.566

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.306

Gnomad4 EAS AF: 0.735

Gnomad4 SAS AF: 0.591

Gnomad4 FIN AF: 0.444

Gnomad4 NFE AF: 0.367

Gnomad4 OTH AF: 0.407

Alfa AF: 0.371 Hom.: 10568

Bravo AF: 0.443

Asia WGS AF: 0.649 AC: 2256 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Sep 11, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.46

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs8192120; hg19: chr5-6632320; COSMIC: COSV52957380; COSMIC: COSV52957380;