chr10-79710623-C-T

Variant names:

• chr10-79710623-C-T
• rs3117557
• NM_001278495.2:c.1593C>T

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2 BP4_Strong BP6_Moderate BP7

The NM_001278495.2(NUTM2B):​c.1593C>T​(p.Ser531Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: not found (cov: 24)
  • Exomes 𝑓: 0.0000024 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: NUTM2B NM_001278495.2 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.115
• Publications: 1 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 -5 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 10-79710623-C-T is Benign according to our data. Variant chr10-79710623-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 3771615.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-0.115 with no splicing effect.

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.1593C>T	p.Ser531Ser	synonymous	Exon 5 of 7	NP_001265424.1	A6NNL0-1
	NUTM2B-AS1	NR_120613.1		n.757-18567G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NUTM2B	ENST00000429828.7	TSL:5 MANE Select	c.1593C>T	p.Ser531Ser	synonymous	Exon 5 of 7	ENSP00000394623.1	A6NNL0-1
	NUTM2B	ENST00000372321.6	TSL:5	c.1593C>T	p.Ser531Ser	synonymous	Exon 5 of 7	ENSP00000361396.2	A6NNL0-2
	NUTM2B-AS1	ENST00000488805.6	TSL:3	n.483-18567G>A		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 24

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000245 AC: 3 AN: 1225392 Hom.: 0 Cov.: 23 AF XY: 0.00000489 AC XY: 3 AN XY: 613016

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

African (AFR) AF: 0.00 AC: 0 AN: 25032

American (AMR) AF: 0.00 AC: 0 AN: 35502

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 23632

East Asian (EAS) AF: 0.00 AC: 0 AN: 33796

South Asian (SAS) AF: 0.00 AC: 0 AN: 75816

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 48066

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3626

European-Non Finnish (NFE) AF: 0.00000215 AC: 2 AN: 928698

Other (OTH) AF: 0.0000195 AC: 1 AN: 51224

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.0000647710), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 24

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

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	-0.91
CADD	Benign	2.0
DANN	Benign	0.49
PhyloP100		-0.12

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: rs3117557; hg19: chr10-81470379;