chr10-14899206-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The ENST00000378289.8(DCLRE1C):c.1263C>G(p.Ser421Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00325 in 702,086 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/14 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 Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SUV39H2 | NM_001193424.2 | c.850-333G>C | intron_variant | ENST00000354919.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SUV39H2 | ENST00000354919.11 | c.850-333G>C | intron_variant | 5 | NM_001193424.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00297 AC: 452AN: 152088Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00254 AC: 325AN: 128082Hom.: 2 AF XY: 0.00254 AC XY: 178AN XY: 70134
GnomAD4 exome AF: 0.00333 AC: 1833AN: 549880Hom.: 8 Cov.: 0 AF XY: 0.00317 AC XY: 944AN XY: 297694
GnomAD4 genome ? AF: 0.00296 AC: 451AN: 152206Hom.: 2 Cov.: 32 AF XY: 0.00251 AC XY: 187AN XY: 74422
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2023 | DCLRE1C: BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at