10-79712337-CTGAAAAGACA-C

Variant names:

• chr10-79712337-CTGAAAAGACA-C
• rs1233867632
• NM_001278495.2:c.2490_2499delTGAAAAGACA

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_001278495.2(NUTM2B):​c.2490_2499delTGAAAAGACA​(p.Glu831ProfsTer15) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.017 (1 hom., cov: 24)
  • Exomes 𝑓: 0.0021 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: NUTM2B NM_001278495.2 frameshift
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.52
• Publications: 0 publications found

Genes affected

NUTM2B (HGNC:23445): (NUT family member 2B)

NUTM2B-AS1 (HGNC:51204): (NUTM2B antisense RNA 1)

ACMG classification

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

• BP6: Variant 10-79712337-CTGAAAAGACA-C is Benign according to our data. Variant chr10-79712337-CTGAAAAGACA-C is described in ClinVar as Benign. ClinVar VariationId is 1301606.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001278495.2. 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
	NUTM2B	NM_001278495.2	MANE Select	c.2490_2499delTGAAAAGACA	p.Glu831ProfsTer15	frameshift	Exon 7 of 7	NP_001265424.1	A6NNL0-1
	NUTM2B-AS1	NR_120613.1		n.757-20291_757-20282delTGTCTTTTCA		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NUTM2B	ENST00000429828.7	TSL:5 MANE Select	c.2490_2499delTGAAAAGACA	p.Glu831ProfsTer15	frameshift	Exon 7 of 7	ENSP00000394623.1	A6NNL0-1
	NUTM2B	ENST00000372321.6	TSL:5	c.1852-556_1852-547delTGAAAAGACA		intron	N/A	ENSP00000361396.2	A6NNL0-2
	NUTM2B-AS1	ENST00000488805.6	TSL:3	n.483-20291_483-20282delTGTCTTTTCA		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0166 AC: 2032 AN: 122230 Hom.: 1 Cov.: 24

Gnomad AFR AF: 0.0754

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00609

Gnomad ASJ AF: 0.00197

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000897

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00787

Gnomad NFE AF: 0.000224

Gnomad OTH AF: 0.00772

GnomAD2 exomes AF: 0.0000271 AC: 5 AN: 184554 AF XY: 0.0000298

Gnomad AFR exome AF: 0.000496

Gnomad AMR exome AF: 0.0000405

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00210 AC: 2750 AN: 1311862 Hom.: 0 AF XY: 0.00183 AC XY: 1197 AN XY: 655254

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0866 AC: 2076 AN: 23986

American (AMR) AF: 0.00323 AC: 132 AN: 40898

Ashkenazi Jewish (ASJ) AF: 0.00231 AC: 54 AN: 23404

East Asian (EAS) AF: 0.00 AC: 0 AN: 35620

South Asian (SAS) AF: 0.000537 AC: 40 AN: 74502

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 51102

Middle Eastern (MID) AF: 0.00360 AC: 14 AN: 3890

European-Non Finnish (NFE) AF: 0.000173 AC: 174 AN: 1004786

Other (OTH) AF: 0.00484 AC: 260 AN: 53674

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0167 AC: 2046 AN: 122270 Hom.: 1 Cov.: 24 AF XY: 0.0163 AC XY: 963 AN XY: 59062

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0758 AC: 1932 AN: 25492

American (AMR) AF: 0.00609 AC: 76 AN: 12486

Ashkenazi Jewish (ASJ) AF: 0.00197 AC: 6 AN: 3050

East Asian (EAS) AF: 0.00 AC: 0 AN: 3554

South Asian (SAS) AF: 0.000900 AC: 3 AN: 3334

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 9118

Middle Eastern (MID) AF: 0.00840 AC: 2 AN: 238

European-Non Finnish (NFE) AF: 0.000224 AC: 14 AN: 62396

Other (OTH) AF: 0.00765 AC: 13 AN: 1700

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00 Hom.: 0

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	Oculopharyngeal myopathy with leukoencephalopathy 1 (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.5
Mutation Taster		=157/43	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs1233867632; hg19: chr10-81472093;