rs4150581
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005316.4(GTF2H1):c.155-31A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.522 in 1,524,534 control chromosomes in the GnomAD database, including 216,994 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.42 ( 15570 hom., cov: 33)
Exomes 𝑓: 0.53 ( 201424 hom. )
Consequence
GTF2H1
NM_005316.4 intron
NM_005316.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.170
Genes affected
GTF2H1 (HGNC:4655): (general transcription factor IIH subunit 1) Enables thyroid hormone receptor binding activity. Involved in positive regulation of transcription, DNA-templated and transcription by RNA polymerase II. Located in nucleoplasm. Part of transcription factor TFIIH core complex and transcription factor TFIIH holo complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GTF2H1 | NM_005316.4 | c.155-31A>G | intron_variant | ENST00000265963.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GTF2H1 | ENST00000265963.9 | c.155-31A>G | intron_variant | 1 | NM_005316.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.418 AC: 63521AN: 152030Hom.: 15570 Cov.: 33
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GnomAD3 exomes AF: 0.477 AC: 115961AN: 242932Hom.: 29202 AF XY: 0.478 AC XY: 62742AN XY: 131334
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GnomAD4 exome AF: 0.533 AC: 731530AN: 1372384Hom.: 201424 Cov.: 20 AF XY: 0.528 AC XY: 362459AN XY: 686998
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GnomAD4 genome ? AF: 0.418 AC: 63533AN: 152150Hom.: 15570 Cov.: 33 AF XY: 0.418 AC XY: 31080AN XY: 74356
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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