chr10-79706577-T-C
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_001278495.2(NUTM2B):āc.918T>Cā(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 (ā ).
Frequency
Genomes: š 0.0019 ( 0 hom., cov: 13)
Exomes š: 0.0013 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
NUTM2B
NM_001278495.2 synonymous
NM_001278495.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.502
Genes affected
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ACMG classification
Classification made for transcript
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: 202AN: 103636Hom.: 0 Cov.: 13 FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00134 AC: 786AN: 585292Hom.: 0 Cov.: 7 AF XY: 0.00130 AC XY: 394AN XY: 302608
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00195 AC: 202AN: 103664Hom.: 0 Cov.: 13 AF XY: 0.00180 AC XY: 86AN XY: 47864
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
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
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at