NM_001351116.2:c.-112-793A>T

Variant names:

• chr10-18655968-T-A
• rs12780826
• NM_001351116.2:c.-112-793A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001351116.2(NSUN6):​c.-112-793A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,254 control chromosomes in the GnomAD database, including 1,302 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.11 (1302 hom., cov: 32)
• Consequence: NSUN6 NM_001351116.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0630
• Publications: 0 publications found

Genes affected

NSUN6 (HGNC:23529): (NOP2/Sun RNA methyltransferase 6) Enables tRNA (cytosine-5-)-methyltransferase activity and tRNA binding activity. Involved in tRNA C5-cytosine methylation. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000302787 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001351116.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NSUN6	NM_001351116.2		c.-112-793A>T		intron	N/A	NP_001338045.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NSUN6	ENST00000414939.1	TSL:3	n.326-793A>T		intron	N/A
	NSUN6	ENST00000444660.1	TSL:4	n.37-793A>T		intron	N/A
	NSUN6	ENST00000449529.1	TSL:2	n.65-793A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16958 AN: 152136 Hom.: 1297 Cov.: 32

Gnomad AFR AF: 0.0270

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.0801

Gnomad EAS AF: 0.0835

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.111 AC: 16969 AN: 152254 Hom.: 1302 Cov.: 32 AF XY: 0.114 AC XY: 8450 AN XY: 74424

African (AFR) AF: 0.0269 AC: 1120 AN: 41566

American (AMR) AF: 0.169 AC: 2584 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0801 AC: 278 AN: 3472

East Asian (EAS) AF: 0.0833 AC: 432 AN: 5184

South Asian (SAS) AF: 0.127 AC: 613 AN: 4824

European-Finnish (FIN) AF: 0.149 AC: 1582 AN: 10604

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 9993 AN: 67996

Other (OTH) AF: 0.104 AC: 220 AN: 2110

Alfa AF: 0.137 Hom.: 213

Bravo AF: 0.107

Asia WGS AF: 0.120 AC: 419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.1
DANN	Benign	0.80
PhyloP100		0.063

Splicing

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

Other links and lift over

dbSNP: rs12780826; hg19: chr10-18944897;