X-24364256-TTGCTGCTGCTGCTGC-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP3BS2
The NM_001136234.3(SUPT20HL1):c.1537_1551delGCTGCTGCTGCTGCT(p.Ala513_Ala517del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00162 in 803,251 control chromosomes in the GnomAD database, including 2 homozygotes. There are 381 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Genomes: 𝑓 0.0041 ( 0 hom., 87 hem., cov: 2)
Exomes 𝑓: 0.0013 ( 2 hom. 294 hem. )
Consequence
SUPT20HL1
NM_001136234.3 conservative_inframe_deletion
NM_001136234.3 conservative_inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.439
Genes affected
SUPT20HL1 (HGNC:30773): (SUPT20H like 1) Predicted to enable transcription coregulator activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be part of SAGA complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP3
Nonframeshift variant in repetitive region in NM_001136234.3
BS2
High Hemizygotes in GnomAd4 at 87 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SUPT20HL1 | NM_001136234.3 | c.1537_1551delGCTGCTGCTGCTGCT | p.Ala513_Ala517del | conservative_inframe_deletion | Exon 1 of 1 | ENST00000686983.1 | NP_001129706.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SUPT20HL1 | ENST00000686983.1 | c.1537_1551delGCTGCTGCTGCTGCT | p.Ala513_Ala517del | conservative_inframe_deletion | Exon 1 of 1 | NM_001136234.3 | ENSP00000509731.1 | |||
SUPT20HL1 | ENST00000436466.2 | c.1537_1551delGCTGCTGCTGCTGCT | p.Ala513_Ala517del | conservative_inframe_deletion | Exon 2 of 2 | 6 | ENSP00000502907.1 |
Frequencies
GnomAD3 genomes AF: 0.00403 AC: 331AN: 82140Hom.: 0 Cov.: 2 AF XY: 0.00441 AC XY: 85AN XY: 19276
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GnomAD4 exome AF: 0.00134 AC: 966AN: 721103Hom.: 2 AF XY: 0.00131 AC XY: 294AN XY: 224973
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GnomAD4 genome AF: 0.00407 AC: 334AN: 82148Hom.: 0 Cov.: 2 AF XY: 0.00451 AC XY: 87AN XY: 19300
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
not provided Uncertain:2
-
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Significance: Uncertain significance
Review Status: no assertion criteria provided
Collection Method: clinical testing
- -
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Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)
Significance: Uncertain significance
Review Status: no assertion criteria provided
Collection Method: clinical testing
- -
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at