rs587784381
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP6BS1BS2
The NM_015559.3(SETBP1):c.46G>A(p.Glu16Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000119 in 1,554,618 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_015559.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000158 AC: 24AN: 152122Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000104 AC: 18AN: 172916Hom.: 0 AF XY: 0.000130 AC XY: 12AN XY: 92178
GnomAD4 exome AF: 0.000115 AC: 161AN: 1402496Hom.: 0 Cov.: 32 AF XY: 0.000111 AC XY: 77AN XY: 691364
GnomAD4 genome AF: 0.000158 AC: 24AN: 152122Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74310
ClinVar
Submissions by phenotype
not provided Benign:2
- -
SETBP1: BP4 -
Schinzel-Giedion syndrome Uncertain:1
- -
Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at