1-155338207-T-G
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_018489.3(ASH1L):āc.8685A>Cā(p.Thr2895=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000359 in 1,614,088 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 (ā ā ).
Frequency
Genomes: š 0.00016 ( 1 hom., cov: 32)
Exomes š: 0.000023 ( 0 hom. )
Consequence
ASH1L
NM_018489.3 synonymous
NM_018489.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.264
Genes affected
ASH1L (HGNC:19088): (ASH1 like histone lysine methyltransferase) This gene encodes a member of the trithorax group of transcriptional activators. The protein contains four AT hooks, a SET domain, a PHD-finger motif, and a bromodomain. It is localized to many small speckles in the nucleus, and also to cell-cell tight junctions. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BP6
Variant 1-155338207-T-G is Benign according to our data. Variant chr1-155338207-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 2639404.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-0.264 with no splicing effect.
BS2
High AC in GnomAd4 at 25 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ASH1L | NM_018489.3 | c.8685A>C | p.Thr2895= | synonymous_variant | 27/28 | ENST00000392403.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ASH1L | ENST00000392403.8 | c.8685A>C | p.Thr2895= | synonymous_variant | 27/28 | 5 | NM_018489.3 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152088Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251494Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135920
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GnomAD4 exome AF: 0.0000226 AC: 33AN: 1461882Hom.: 0 Cov.: 31 AF XY: 0.0000248 AC XY: 18AN XY: 727246
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GnomAD4 genome AF: 0.000164 AC: 25AN: 152206Hom.: 1 Cov.: 32 AF XY: 0.000188 AC XY: 14AN XY: 74424
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 01, 2023 | ASH1L: BP4, BP7 - |
ASH1L-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 06, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
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DANN
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at