NM_199044.4:c.-57A>T

Variant names:

• chr1-46340770-A-T
• rs1662030822
• NM_199044.4:c.-57A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_199044.4(NSUN4):​c.-57A>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: NSUN4 NM_199044.4 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.43
• Publications: 0 publications found

Genes affected

NSUN4 (HGNC:31802): (NOP2/Sun RNA methyltransferase 4) Enables rRNA (cytosine-C5-)-methyltransferase activity. Involved in rRNA methylation. Part of mitochondrial large ribosomal subunit. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_199044.4. 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
	NSUN4	NM_199044.4	MANE Select	c.-57A>T		upstream_gene	N/A	NP_950245.2
	NSUN4	NM_001387265.1		c.-57A>T		upstream_gene	N/A	NP_001374194.1
	NSUN4	NM_001387266.1		c.-57A>T		upstream_gene	N/A	NP_001374195.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NSUN4	ENST00000474844.6	TSL:1 MANE Select	c.-57A>T		upstream_gene	N/A	ENSP00000419740.1
	NSUN4	ENST00000307089.7	TSL:1	n.-57A>T		upstream_gene	N/A	ENSP00000471937.1
	NSUN4	ENST00000469918.5	TSL:3	n.-57A>T		upstream_gene	N/A	ENSP00000478949.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1322936 Hom.: 0 Cov.: 19 AF XY: 0.00 AC XY: 0 AN XY: 656918

African (AFR) AF: 0.00 AC: 0 AN: 29318

American (AMR) AF: 0.00 AC: 0 AN: 30796

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 22696

East Asian (EAS) AF: 0.00 AC: 0 AN: 35976

South Asian (SAS) AF: 0.00 AC: 0 AN: 76798

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 50154

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4688

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1017520

Other (OTH) AF: 0.00 AC: 0 AN: 54990

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	18
DANN	Benign	0.81
PhyloP100		2.4
PromoterAI		-0.36	Neutral

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

Other links and lift over

dbSNP: rs1662030822; hg19: chr1-46806442;