chr1-150950463-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 1P and 14B. PP2BP4_StrongBP6_ModerateBS1BS2
The NM_001366418.1(SETDB1):c.1589C>T(p.Pro530Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00253 in 1,593,386 control chromosomes in the GnomAD database, including 49 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001366418.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SETDB1 | NM_001366418.1 | c.1589C>T | p.Pro530Leu | missense_variant | 13/22 | ENST00000692827.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SETDB1 | ENST00000692827.1 | c.1589C>T | p.Pro530Leu | missense_variant | 13/22 | NM_001366418.1 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00187 AC: 285AN: 152142Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00379 AC: 886AN: 233482Hom.: 9 AF XY: 0.00499 AC XY: 630AN XY: 126286
GnomAD4 exome AF: 0.00260 AC: 3750AN: 1441126Hom.: 48 Cov.: 32 AF XY: 0.00328 AC XY: 2351AN XY: 715788
GnomAD4 genome ? AF: 0.00187 AC: 285AN: 152260Hom.: 1 Cov.: 32 AF XY: 0.00203 AC XY: 151AN XY: 74440
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at