10-79711875-T-C
Position:
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6
The NM_001278495.2(NUTM2B):āc.2027T>Cā(p.Met676Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: š 0.052 ( 494 hom., cov: 27)
Exomes š: 0.039 ( 21142 hom. )
Failed GnomAD Quality Control
Consequence
NUTM2B
NM_001278495.2 missense
NM_001278495.2 missense
Scores
17
Clinical Significance
Conservation
PhyloP100: -4.51
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.004448861).
BP6
Variant 10-79711875-T-C is Benign according to our data. Variant chr10-79711875-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 1206196.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr10-79711875-T-C is described in Lovd as [Benign]. Variant chr10-79711875-T-C is described in Lovd as [Likely_benign].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NUTM2B | NM_001278495.2 | c.2027T>C | p.Met676Thr | missense_variant | 7/7 | ENST00000429828.7 | |
NUTM2B-AS1 | NR_120613.1 | n.757-19819A>G | intron_variant, non_coding_transcript_variant | ||||
NUTM2B | XM_047425707.1 | c.2027T>C | p.Met676Thr | missense_variant | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUTM2B | ENST00000429828.7 | c.2027T>C | p.Met676Thr | missense_variant | 7/7 | 5 | NM_001278495.2 | P1 | |
NUTM2B-AS1 | ENST00000671459.1 | n.146-48641A>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 5707AN: 110256Hom.: 491 Cov.: 27 FAILED QC
GnomAD3 genomes
AF:
AC:
5707
AN:
110256
Hom.:
Cov.:
27
FAILED QC
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.0175 AC: 3797AN: 216746Hom.: 1866 AF XY: 0.0164 AC XY: 1923AN XY: 117070
GnomAD3 exomes
AF:
AC:
3797
AN:
216746
Hom.:
AF XY:
AC XY:
1923
AN XY:
117070
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0387 AC: 50687AN: 1309642Hom.: 21142 Cov.: 34 AF XY: 0.0450 AC XY: 29196AN XY: 648570
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
50687
AN:
1309642
Hom.:
Cov.:
34
AF XY:
AC XY:
29196
AN XY:
648570
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0519 AC: 5724AN: 110296Hom.: 494 Cov.: 27 AF XY: 0.0525 AC XY: 2800AN XY: 53298
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
5724
AN:
110296
Hom.:
Cov.:
27
AF XY:
AC XY:
2800
AN XY:
53298
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
ExAC
AF:
AC:
3
ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
not provided Benign:1
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N;N
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Vest4
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at