14-74909626-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_031464.5(RPS6KL1):c.1187T>C(p.Met396Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000049 in 1,611,912 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_031464.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPS6KL1 | NM_031464.5 | c.1187T>C | p.Met396Thr | missense_variant | 8/12 | ENST00000557413.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPS6KL1 | ENST00000557413.6 | c.1187T>C | p.Met396Thr | missense_variant | 8/12 | 5 | NM_031464.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000309 AC: 47AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000102 AC: 25AN: 246264Hom.: 0 AF XY: 0.0000819 AC XY: 11AN XY: 134274
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1459722Hom.: 0 Cov.: 32 AF XY: 0.0000207 AC XY: 15AN XY: 726260
GnomAD4 genome ? AF: 0.000309 AC: 47AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.000430 AC XY: 32AN XY: 74350
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 08, 2022 | 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