9-128683961-G-T
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The ENST00000372692.8(SET):c.66G>T(p.Leu22=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00223 in 1,557,270 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0059 ( 8 hom., cov: 31)
Exomes 𝑓: 0.0018 ( 10 hom. )
Consequence
SET
ENST00000372692.8 synonymous
ENST00000372692.8 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.399
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]
HMGA1P4 (HGNC:39093): (high mobility group AT-hook 1 pseudogene 4)
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
?
Variant 9-128683961-G-T is Benign according to our data. Variant chr9-128683961-G-T is described in ClinVar as [Benign]. Clinvar id is 774204.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
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Synonymous conserved (PhyloP=-0.399 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4_exome allele frequency = 0.00182 (2563/1405018) while in subpopulation AFR AF= 0.018 (573/31820). AF 95% confidence interval is 0.0168. There are 10 homozygotes in gnomad4_exome. There are 1228 alleles in male gnomad4_exome subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 902 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SET | NM_001122821.2 | c.66G>T | p.Leu22= | synonymous_variant | 1/8 | ||
SET | NM_001374326.1 | c.66G>T | p.Leu22= | synonymous_variant | 2/9 | ||
DYNC2I2 | XM_011519179.3 | c.-133+405C>A | intron_variant | ||||
DYNC2I2 | XM_047424057.1 | c.-133+405C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HMGA1P4 | ENST00000652876.3 | n.128+405C>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00595 AC: 905AN: 152134Hom.: 8 Cov.: 31
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GnomAD3 exomes AF: 0.00296 AC: 483AN: 163212Hom.: 3 AF XY: 0.00261 AC XY: 227AN XY: 86836
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GnomAD4 exome AF: 0.00182 AC: 2563AN: 1405018Hom.: 10 Cov.: 30 AF XY: 0.00177 AC XY: 1228AN XY: 693576
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GnomAD4 genome ? AF: 0.00592 AC: 902AN: 152252Hom.: 8 Cov.: 31 AF XY: 0.00576 AC XY: 429AN XY: 74438
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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 | Invitae | Dec 31, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at