chr10-14899283-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM2BP4_ModerateBP6_ModerateBS1
The ENST00000378289.8(DCLRE1C):c.1186C>T(p.Arg396Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000117 in 702,088 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
ENST00000378289.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SUV39H2 | NM_001193424.2 | c.850-256G>A | intron_variant | ENST00000354919.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SUV39H2 | ENST00000354919.11 | c.850-256G>A | intron_variant | 5 | NM_001193424.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000283 AC: 43AN: 151958Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000780 AC: 10AN: 128284Hom.: 0 AF XY: 0.0000855 AC XY: 6AN XY: 70194
GnomAD4 exome AF: 0.0000709 AC: 39AN: 550012Hom.: 1 Cov.: 4 AF XY: 0.0000705 AC XY: 21AN XY: 297760
GnomAD4 genome ? AF: 0.000283 AC: 43AN: 152076Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74334
ClinVar
Submissions by phenotype
DCLRE1C-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 20, 2019 | 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). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at