rs17353856
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1
The NM_001193424.2(SUV39H2):c.966C>T(p.Tyr322=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 1,613,652 control chromosomes in the GnomAD database, including 13,659 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 0.095 ( 882 hom., cov: 32)
Exomes 𝑓: 0.13 ( 12777 hom. )
Consequence
SUV39H2
NM_001193424.2 synonymous
NM_001193424.2 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.128
Genes affected
SUV39H2 (HGNC:17287): (SUV39H2 histone lysine methyltransferase) Enables S-adenosyl-L-methionine binding activity; histone methyltransferase activity (H3-K9 specific); and zinc ion binding activity. Involved in chromatin assembly or disassembly and chromatin remodeling. Acts upstream of or within cellular response to hypoxia and negative regulation of transcription by RNA polymerase II. Located in chromatin. [provided by Alliance of Genome Resources, Apr 2022]
DCLRE1C (HGNC:17642): (DNA cross-link repair 1C) This gene encodes a nuclear protein that is involved in V(D)J recombination and DNA repair. The encoded protein has single-strand-specific 5'-3' exonuclease activity; it also exhibits endonuclease activity on 5' and 3' overhangs and hairpins. The protein also functions in the regulation of the cell cycle in response to DNA damage. Mutations in this gene can cause Athabascan-type severe combined immunodeficiency (SCIDA) and Omenn syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.39).
BP7
?
Synonymous conserved (PhyloP=0.128 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SUV39H2 | NM_001193424.2 | c.966C>T | p.Tyr322= | synonymous_variant | 4/6 | ENST00000354919.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SUV39H2 | ENST00000354919.11 | c.966C>T | p.Tyr322= | synonymous_variant | 4/6 | 5 | NM_001193424.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0954 AC: 14515AN: 152096Hom.: 882 Cov.: 32
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GnomAD3 exomes AF: 0.105 AC: 26228AN: 250970Hom.: 1626 AF XY: 0.105 AC XY: 14255AN XY: 135642
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GnomAD4 exome AF: 0.128 AC: 186402AN: 1461438Hom.: 12777 Cov.: 32 AF XY: 0.126 AC XY: 91663AN XY: 727000
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GnomAD4 genome ? AF: 0.0953 AC: 14512AN: 152214Hom.: 882 Cov.: 32 AF XY: 0.0957 AC XY: 7124AN XY: 74406
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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
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at