chr10-14899187-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The ENST00000378289.8(DCLRE1C):c.1282C>T(p.Arg428Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00332 in 701,848 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/13 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 Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SUV39H2 | NM_001193424.2 | c.850-352G>A | intron_variant | ENST00000354919.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SUV39H2 | ENST00000354919.11 | c.850-352G>A | intron_variant | 5 | NM_001193424.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00289 AC: 440AN: 152100Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.00343 AC: 438AN: 127866Hom.: 4 AF XY: 0.00356 AC XY: 249AN XY: 70018
GnomAD4 exome AF: 0.00344 AC: 1888AN: 549630Hom.: 9 Cov.: 0 AF XY: 0.00349 AC XY: 1039AN XY: 297552
GnomAD4 genome ? AF: 0.00289 AC: 440AN: 152218Hom.: 3 Cov.: 32 AF XY: 0.00259 AC XY: 193AN XY: 74416
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 01, 2023 | DCLRE1C: BP4, BS2; SUV39H2: BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at