11-34112124-C-T
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_024662.3(NAT10):c.273C>T(p.Asp91Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000756 in 1,614,202 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00046 ( 1 hom., cov: 33)
Exomes 𝑓: 0.000036 ( 0 hom. )
Consequence
NAT10
NM_024662.3 synonymous
NM_024662.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.82
Genes affected
NAT10 (HGNC:29830): (N-acetyltransferase 10) The protein encoded by this gene is an RNA cytidine acetyltransferase involved in histone acetylation, tRNA acetylation, the biosynthesis of 18S rRNA, and the enhancement of nuclear architecture and chromatin organization. [provided by RefSeq, Oct 2016]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.34).
BP6
Variant 11-34112124-C-T is Benign according to our data. Variant chr11-34112124-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 732327.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.82 with no splicing effect.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NAT10 | ENST00000257829.8 | c.273C>T | p.Asp91Asp | synonymous_variant | Exon 4 of 29 | 1 | NM_024662.3 | ENSP00000257829.3 | ||
NAT10 | ENST00000531159.6 | c.57C>T | p.Asp19Asp | synonymous_variant | Exon 2 of 27 | 2 | ENSP00000433011.2 | |||
NAT10 | ENST00000527971.5 | c.273C>T | p.Asp91Asp | synonymous_variant | Exon 3 of 8 | 2 | ENSP00000437324.1 | |||
NAT10 | ENST00000529523.5 | c.273C>T | p.Asp91Asp | synonymous_variant | Exon 4 of 5 | 4 | ENSP00000435569.1 |
Frequencies
GnomAD3 genomes AF: 0.000460 AC: 70AN: 152196Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.000103 AC: 26AN: 251380Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135852
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GnomAD4 exome AF: 0.0000356 AC: 52AN: 1461888Hom.: 0 Cov.: 31 AF XY: 0.0000358 AC XY: 26AN XY: 727246
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GnomAD4 genome AF: 0.000460 AC: 70AN: 152314Hom.: 1 Cov.: 33 AF XY: 0.000389 AC XY: 29AN XY: 74482
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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
Feb 20, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Name
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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