rs1344642
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000295709.8(STK36):c.1748G>A(p.Arg583Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.437 in 1,612,946 control chromosomes in the GnomAD database, including 159,073 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R583W) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000295709.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
STK36 | NM_015690.5 | c.1748G>A | p.Arg583Gln | missense_variant | 14/27 | ENST00000295709.8 | NP_056505.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
STK36 | ENST00000295709.8 | c.1748G>A | p.Arg583Gln | missense_variant | 14/27 | 1 | NM_015690.5 | ENSP00000295709 | P1 |
Frequencies
GnomAD3 genomes AF: 0.482 AC: 73247AN: 151902Hom.: 18751 Cov.: 32
GnomAD3 exomes AF: 0.413 AC: 103838AN: 251210Hom.: 22959 AF XY: 0.409 AC XY: 55487AN XY: 135778
GnomAD4 exome AF: 0.432 AC: 631525AN: 1460926Hom.: 140271 Cov.: 37 AF XY: 0.428 AC XY: 311188AN XY: 726824
GnomAD4 genome AF: 0.483 AC: 73359AN: 152020Hom.: 18802 Cov.: 32 AF XY: 0.475 AC XY: 35284AN XY: 74308
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 04, 2021 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at