NM_001355263.2:c.1126C>T

Variant names:

• chr10-79846873-C-T
• rs1842024251
• NM_001355263.2:c.1126C>T

Variant summary

Our verdict is Benign. The variant received -7 ACMG points: 0P and 7B. BP4_Strong BP6_Moderate BP7

The NM_001355263.2(NUTM2E):​c.1126C>T​(p.Leu376Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: not found (cov: 16)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: NUTM2E NM_001355263.2 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.522
• Publications: 0 publications found

Genes affected

NUTM2E (HGNC:23448): (NUT family member 2E)

ACMG classification

Our verdict: Benign. The variant received -7 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BP6: Variant 10-79846873-C-T is Benign according to our data. Variant chr10-79846873-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2640647.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=0.522 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001355263.2. 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
	NUTM2E	NM_001355263.2	MANE Select	c.1126C>T	p.Leu376Leu	synonymous	Exon 6 of 10	NP_001342192.1	B1AL46

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NUTM2E	ENST00000429984.5	TSL:5 MANE Select	c.1126C>T	p.Leu376Leu	synonymous	Exon 6 of 10	ENSP00000407521.2	B1AL46
	NUTM2E	ENST00000602967.5	TSL:5	c.1126C>T	p.Leu376Leu	synonymous	Exon 3 of 6	ENSP00000473558.1	R4GNA6

Frequencies

GnomAD3 genomes Cov.: 16

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 716786 Hom.: 0 Cov.: 9 AF XY: 0.00 AC XY: 0 AN XY: 366362

African (AFR) AF: 0.00 AC: 0 AN: 21122

American (AMR) AF: 0.00 AC: 0 AN: 29270

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 17802

East Asian (EAS) AF: 0.00 AC: 0 AN: 32226

South Asian (SAS) AF: 0.00 AC: 0 AN: 65012

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 34300

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2722

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 479982

Other (OTH) AF: 0.00 AC: 0 AN: 34350

GnomAD4 genome Cov.: 16

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	4.6
DANN	Benign	0.72
PhyloP100		0.52

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: rs1842024251; hg19: chr10-81606629;