9-94318482-G-T

Variant names:

• chr9-94318482-G-T
• rs775569752
• NM_017561.2:c.2254C>A

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP4_Strong BP7

The NM_017561.2(NUTM2F):​c.2254C>A​(p.Arg752Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. 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: 10)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: NUTM2F NM_017561.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.815
• Publications: 0 publications found

Genes affected

NUTM2F (HGNC:23450): (NUT family member 2F)

LOC105376154 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -5 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BP7: Synonymous conserved (PhyloP=0.815 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017561.2. 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
	NUTM2F	NM_017561.2	MANE Select	c.2254C>A	p.Arg752Arg	synonymous	Exon 7 of 7	NP_060031.1	A1L443

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NUTM2F	ENST00000253262.9	TSL:1 MANE Select	c.2254C>A	p.Arg752Arg	synonymous	Exon 7 of 7	ENSP00000253262.4	A1L443

Frequencies

GnomAD3 genomes Cov.: 10

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 762448 Hom.: 0 Cov.: 10 AF XY: 0.00 AC XY: 0 AN XY: 392538

African (AFR) AF: 0.00 AC: 0 AN: 22072

American (AMR) AF: 0.00 AC: 0 AN: 29122

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18152

East Asian (EAS) AF: 0.00 AC: 0 AN: 33492

South Asian (SAS) AF: 0.00 AC: 0 AN: 60022

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 42746

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2740

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 517182

Other (OTH) AF: 0.00 AC: 0 AN: 36920

GnomAD4 genome Cov.: 10

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.49
PhyloP100		0.81

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: rs775569752; hg19: chr9-97080764;