6-158170446-A-G
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_207118.3(GTF2H5):c.-34-24A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0429 in 1,365,594 control chromosomes in the GnomAD database, including 2,916 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). There are indicators that this mutation may affect the branch point..
Frequency
Genomes: 𝑓 0.043 ( 382 hom., cov: 32)
Exomes 𝑓: 0.043 ( 2534 hom. )
Consequence
GTF2H5
NM_207118.3 intron
NM_207118.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.636
Genes affected
GTF2H5 (HGNC:21157): (general transcription factor IIH subunit 5) This gene encodes a subunit of transcription/repair factor TFIIH, which functions in gene transcription and DNA repair. This protein stimulates ERCC3/XPB ATPase activity to trigger DNA opening during DNA repair, and is implicated in regulating cellular levels of TFIIH. Mutations in this gene result in trichothiodystrophy, complementation group A. [provided by RefSeq, Mar 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
This place is a probable branch point but likely benign (scored 3 / 10). Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
Variant 6-158170446-A-G is Benign according to our data. Variant chr6-158170446-A-G is described in ClinVar as [Benign]. Clinvar id is 1270314.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GTF2H5 | NM_207118.3 | c.-34-24A>G | intron_variant | ENST00000607778.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GTF2H5 | ENST00000607778.2 | c.-34-24A>G | intron_variant | 1 | NM_207118.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0434 AC: 6602AN: 152150Hom.: 379 Cov.: 32
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GnomAD4 exome AF: 0.0429 AC: 52006AN: 1213326Hom.: 2534 Cov.: 17 AF XY: 0.0412 AC XY: 25390AN XY: 616420
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GnomAD4 genome AF: 0.0434 AC: 6612AN: 152268Hom.: 382 Cov.: 32 AF XY: 0.0454 AC XY: 3382AN XY: 74450
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 09, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
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Benign
DANN
Benign
BranchPoint Hunter
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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