chrX-48695823-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PP2BP4_StrongBP6_ModerateBS2
The NM_001282166.2(SUV39H1):c.4G>A(p.Val2Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000883 in 1,042,081 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 50 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 10/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001282166.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SUV39H1 | NM_001282166.2 | c.4G>A | p.Val2Met | missense_variant | 1/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SUV39H1 | ENST00000337852.10 | c.4G>A | p.Val2Met | missense_variant | 1/6 | 2 |
Frequencies
GnomAD3 genomes Cov.: 24
GnomAD3 exomes AF: 0.000235 AC: 22AN: 93446Hom.: 0 AF XY: 0.000455 AC XY: 16AN XY: 35156
GnomAD4 exome AF: 0.0000883 AC: 92AN: 1042081Hom.: 0 Cov.: 31 AF XY: 0.000147 AC XY: 50AN XY: 341261
GnomAD4 genome Cov.: 24
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2022 | SUV39H1: PP2, PP3, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at