9-128690034-C-T
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_003011.4(SET):c.73+379C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00111 in 1,024,120 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 Benign (★).
Frequency
Genomes: 𝑓 0.00082 ( 0 hom., cov: 30)
Exomes 𝑓: 0.0012 ( 1 hom. )
Consequence
SET
NM_003011.4 intron
NM_003011.4 intron
Scores
1
1
Splicing: ADA: 0.0001700
2
Clinical Significance
Conservation
PhyloP100: 0.152
Genes affected
SET (HGNC:10760): (SET nuclear proto-oncogene) The protein encoded by this gene inhibits acetylation of nucleosomes, especially histone H4, by histone acetylases (HAT). This inhibition is most likely accomplished by masking histone lysines from being acetylated, and the consequence is to silence HAT-dependent transcription. The encoded protein is part of a complex localized to the endoplasmic reticulum but is found in the nucleus and inhibits apoptosis following attack by cytotoxic T lymphocytes. This protein can also enhance DNA replication of the adenovirus genome. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.49).
BP6
?
Variant 9-128690034-C-T is Benign according to our data. Variant chr9-128690034-C-T is described in ClinVar as [Benign]. Clinvar id is 1711695.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd4 at 120 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SET | NM_003011.4 | c.73+379C>T | intron_variant | ENST00000322030.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SET | ENST00000322030.13 | c.73+379C>T | intron_variant | 1 | NM_003011.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000821 AC: 120AN: 146114Hom.: 0 Cov.: 30
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GnomAD3 exomes AF: 0.00110 AC: 29AN: 26270Hom.: 0 AF XY: 0.00124 AC XY: 20AN XY: 16146
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GnomAD4 exome AF: 0.00116 AC: 1017AN: 878006Hom.: 1 Cov.: 18 AF XY: 0.00125 AC XY: 518AN XY: 415416
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GnomAD4 genome ? AF: 0.000821 AC: 120AN: 146114Hom.: 0 Cov.: 30 AF XY: 0.000703 AC XY: 50AN XY: 71090
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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 | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2024 | SET: BS1, BS2 - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at