NM_017970.4:c.1842+150C>T

Variant names:

• chr14-90292547-G-A
• rs2282032
• NM_017970.4:c.1842+150C>T

Variant summary

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

The NM_017970.4(NRDE2):​c.1842+150C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000161 in 622,698 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 0.0000016 (0 hom.)
• Consequence: NRDE2 NM_017970.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.56
• Publications: 0 publications found

Genes affected

NRDE2 (HGNC:20186): (NRDE-2, necessary for RNA interference, domain containing) Involved in several processes, including RNA splicing; negative regulation of RNA catabolic process; and positive regulation of RNA export from nucleus. Located in nuclear speck and nucleolus. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000287437 (HGNC:):

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=-0.83).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017970.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NRDE2	NM_017970.4	MANE Select	c.1842+150C>T		intron	N/A	NP_060440.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NRDE2	ENST00000354366.8	TSL:1 MANE Select	c.1842+150C>T		intron	N/A	ENSP00000346335.3	Q9H7Z3
	NRDE2	ENST00000553409.5	TSL:1	n.*1367+150C>T		intron	N/A	ENSP00000451025.1	G3V338
	NRDE2	ENST00000556189.5	TSL:1	n.*320+150C>T		intron	N/A	ENSP00000452107.1	H0YJT6

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000161 AC: 1 AN: 622698 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 320740

African (AFR) AF: 0.00 AC: 0 AN: 15986

American (AMR) AF: 0.00 AC: 0 AN: 20980

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14798

East Asian (EAS) AF: 0.0000303 AC: 1 AN: 32966

South Asian (SAS) AF: 0.00 AC: 0 AN: 49010

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 34624

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2268

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 420292

Other (OTH) AF: 0.00 AC: 0 AN: 31774

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.2
DANN	Benign	0.60
PhyloP100		1.6

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: rs2282032; hg19: chr14-90758891;