chr1-150961124-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.3065C>T(p.Ala1022Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00425 in 1,614,036 control chromosomes in the GnomAD database, including 152 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.3065C>T | p.Ala1022Val | missense_variant | 16/22 | ENST00000692827.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SETDB1 | ENST00000692827.1 | c.3065C>T | p.Ala1022Val | missense_variant | 16/22 | NM_001366418.1 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0106 AC: 1615AN: 152116Hom.: 28 Cov.: 31
GnomAD3 exomes AF: 0.00773 AC: 1942AN: 251266Hom.: 40 AF XY: 0.00888 AC XY: 1207AN XY: 135854
GnomAD4 exome AF: 0.00358 AC: 5237AN: 1461804Hom.: 124 Cov.: 33 AF XY: 0.00448 AC XY: 3255AN XY: 727204
GnomAD4 genome AF: 0.0106 AC: 1619AN: 152232Hom.: 28 Cov.: 31 AF XY: 0.0113 AC XY: 843AN XY: 74424
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