10-79706577-T-C

Position:

• chr10-79706577-T-C

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The NM_001278495.2(NUTM2B):​c.918T>C​(p.His306=) 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: 𝑓 0.0019 (0 hom., cov: 13)
  • Exomes 𝑓: 0.0013 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: NUTM2B NM_001278495.2 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.502

Genes affected

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

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

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BP6: Variant 10-79706577-T-C is Benign according to our data. Variant chr10-79706577-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 3025690.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NUTM2B	NM_001278495.2	c.918T>C	p.His306=	synonymous_variant	2/7	ENST00000429828.7
NUTM2B-AS1	NR_120613.1	n.757-14521A>G		intron_variant, non_coding_transcript_variant
NUTM2B	XM_047425707.1	c.918T>C	p.His306=	synonymous_variant	4/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NUTM2B	ENST00000429828.7	c.918T>C	p.His306=	synonymous_variant	2/7	5	NM_001278495.2	P1
NUTM2B-AS1	ENST00000671459.1	n.146-43343A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.00 AC: 202 AN: 103636 Hom.: 0 Cov.: 13 FAILED QC

Gnomad AFR AF: 0.000839

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00130

Gnomad ASJ AF: 0.00285

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000389

Gnomad FIN AF: 0.000306

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00300

Gnomad OTH AF: 0.000744

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00134 AC: 786 AN: 585292 Hom.: 0 Cov.: 7 AF XY: 0.00130 AC XY: 394 AN XY: 302608

Gnomad4 AFR exome AF: 0.000338

Gnomad4 AMR exome AF: 0.000817

Gnomad4 ASJ exome AF: 0.00224

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000245

Gnomad4 FIN exome AF: 0.000167

Gnomad4 NFE exome AF: 0.00172

Gnomad4 OTH exome AF: 0.00138

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00195 AC: 202 AN: 103664 Hom.: 0 Cov.: 13 AF XY: 0.00180 AC XY: 86 AN XY: 47864

Gnomad4 AFR AF: 0.000837

Gnomad4 AMR AF: 0.00130

Gnomad4 ASJ AF: 0.00285

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000392

Gnomad4 FIN AF: 0.000306

Gnomad4 NFE AF: 0.00300

Gnomad4 OTH AF: 0.000735

Alfa AF: 0.00202 Hom.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Nov 01, 2023

NUTM2B: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.6
DANN	Benign	0.42

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1172700128; hg19: chr10-81466333;