14-21352783-GTTC-G
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PM4_SupportingBP6BS2
The NM_007192.4(SUPT16H):c.3031_3033delGAA(p.Glu1011del) variant causes a conservative inframe deletion change. The variant allele was found at a frequency of 0.0000347 in 1,613,836 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000037 ( 0 hom. )
Consequence
SUPT16H
NM_007192.4 conservative_inframe_deletion
NM_007192.4 conservative_inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 4.58
Genes affected
SUPT16H (HGNC:11465): (SPT16 homolog, facilitates chromatin remodeling subunit) Transcription of protein-coding genes can be reconstituted on naked DNA with only the general transcription factors and RNA polymerase II. However, this minimal system cannot transcribe DNA packaged into chromatin, indicating that accessory factors may facilitate access to DNA. One such factor, FACT (facilitates chromatin transcription), interacts specifically with histones H2A/H2B to effect nucleosome disassembly and transcription elongation. FACT is composed of an 80 kDa subunit and a 140 kDa subunit; this gene encodes the 140 kDa subunit. [provided by RefSeq, Feb 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM4
Nonframeshift variant in NON repetitive region in NM_007192.4. Strenght limited to Supporting due to length of the change: 1aa.
BP6
Variant 14-21352783-GTTC-G is Benign according to our data. Variant chr14-21352783-GTTC-G is described in ClinVar as [Likely_benign]. Clinvar id is 3030422.Status of the report is no_assertion_criteria_provided, 0 stars.
BS2
High AC in GnomAdExome4 at 54 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SUPT16H | NM_007192.4 | c.3031_3033delGAA | p.Glu1011del | conservative_inframe_deletion | 26/26 | ENST00000216297.7 | NP_009123.1 | |
SUPT16H | XM_047430899.1 | c.2836_2838delGAA | p.Glu946del | conservative_inframe_deletion | 25/25 | XP_047286855.1 |
Ensembl
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GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151952Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000161 AC: 4AN: 249166Hom.: 0 AF XY: 0.00000741 AC XY: 1AN XY: 134864
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GnomAD4 exome AF: 0.0000369 AC: 54AN: 1461884Hom.: 0 AF XY: 0.0000440 AC XY: 32AN XY: 727246
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GnomAD4 genome AF: 0.0000132 AC: 2AN: 151952Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74208
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
SUPT16H-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 23, 2024 | 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). - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at