chr14-90872121-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_004755.4(RPS6KA5):āc.2362A>Gā(p.Ser788Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,613,738 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_004755.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPS6KA5 | NM_004755.4 | c.2362A>G | p.Ser788Gly | missense_variant | 17/17 | ENST00000614987.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPS6KA5 | ENST00000614987.5 | c.2362A>G | p.Ser788Gly | missense_variant | 17/17 | 1 | NM_004755.4 | P1 | |
RPS6KA5 | ENST00000536315.6 | c.2125A>G | p.Ser709Gly | missense_variant | 17/17 | 2 | |||
RPS6KA5 | ENST00000556178.5 | c.*1832A>G | 3_prime_UTR_variant, NMD_transcript_variant | 14/14 | 5 | ||||
RPS6KA5 | ENST00000648062.1 | c.*1988A>G | 3_prime_UTR_variant, NMD_transcript_variant | 19/19 |
Frequencies
GnomAD3 genomes AF: 0.00000659 AC: 1AN: 151826Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000637 AC: 16AN: 251054Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135650
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1461794Hom.: 0 Cov.: 31 AF XY: 0.0000248 AC XY: 18AN XY: 727200
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151944Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74272
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 05, 2023 | 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