5-6599379-TG-T

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

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.834
Variant links:
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]
LINC01018 (HGNC:27394): (long intergenic non-protein coding RNA 1018)

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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
NSUN2NM_017755.6 linkuse as main transcriptc.*546del 3_prime_UTR_variant 19/19 ENST00000264670.11
NSUN2NM_001193455.2 linkuse as main transcriptc.*546del 3_prime_UTR_variant 18/18
NSUN2NR_037947.2 linkuse as main transcriptn.2830del non_coding_transcript_exon_variant 18/18

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NSUN2ENST00000264670.11 linkuse as main transcriptc.*546del 3_prime_UTR_variant 19/191 NM_017755.6 P2Q08J23-1
LINC01018ENST00000661215.1 linkuse as main transcriptn.757-739del intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.0396
AC:
6021
AN:
152148
Hom.:
147
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0184
Gnomad AMI
AF:
0.0702
Gnomad AMR
AF:
0.0353
Gnomad ASJ
AF:
0.0409
Gnomad EAS
AF:
0.000385
Gnomad SAS
AF:
0.0350
Gnomad FIN
AF:
0.0328
Gnomad MID
AF:
0.0538
Gnomad NFE
AF:
0.0573
Gnomad OTH
AF:
0.0369
GnomAD4 exome
AF:
0.0399
AC:
23
AN:
576
Hom.:
0
Cov.:
0
AF XY:
0.0460
AC XY:
16
AN XY:
348
show subpopulations
Gnomad4 AMR exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.0370
Gnomad4 NFE exome
AF:
0.0556
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0395
AC:
6022
AN:
152266
Hom.:
147
Cov.:
32
AF XY:
0.0385
AC XY:
2868
AN XY:
74452
show subpopulations
Gnomad4 AFR
AF:
0.0184
Gnomad4 AMR
AF:
0.0352
Gnomad4 ASJ
AF:
0.0409
Gnomad4 EAS
AF:
0.000386
Gnomad4 SAS
AF:
0.0354
Gnomad4 FIN
AF:
0.0328
Gnomad4 NFE
AF:
0.0573
Gnomad4 OTH
AF:
0.0365
Alfa
AF:
0.0471
Hom.:
31
Bravo
AF:
0.0390
Asia WGS
AF:
0.0170
AC:
59
AN:
3478

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 submitterclinical testingIllumina Laboratory Services, IlluminaJun 14, 2016- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs200230801; hg19: chr5-6599492; API