14-90872123-T-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_004755.4(RPS6KA5):c.2360A>T(p.Asp787Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000403 in 1,613,680 control chromosomes in the GnomAD database, including 1 homozygotes. 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 Uncertain significance (★).
Frequency
Consequence
NM_004755.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPS6KA5 | NM_004755.4 | c.2360A>T | p.Asp787Val | missense_variant | 17/17 | ENST00000614987.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPS6KA5 | ENST00000614987.5 | c.2360A>T | p.Asp787Val | missense_variant | 17/17 | 1 | NM_004755.4 | P1 | |
RPS6KA5 | ENST00000536315.6 | c.2123A>T | p.Asp708Val | missense_variant | 17/17 | 2 | |||
RPS6KA5 | ENST00000556178.5 | c.*1830A>T | 3_prime_UTR_variant, NMD_transcript_variant | 14/14 | 5 | ||||
RPS6KA5 | ENST00000648062.1 | c.*1986A>T | 3_prime_UTR_variant, NMD_transcript_variant | 19/19 |
Frequencies
GnomAD3 genomes ? AF: 0.0000395 AC: 6AN: 151760Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000717 AC: 18AN: 251034Hom.: 0 AF XY: 0.0000737 AC XY: 10AN XY: 135646
GnomAD4 exome AF: 0.0000404 AC: 59AN: 1461802Hom.: 1 Cov.: 31 AF XY: 0.0000426 AC XY: 31AN XY: 727200
GnomAD4 genome ? AF: 0.0000395 AC: 6AN: 151878Hom.: 0 Cov.: 31 AF XY: 0.0000674 AC XY: 5AN XY: 74222
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 18, 2023 | The c.2360A>T (p.D787V) alteration is located in exon 17 (coding exon 17) of the RPS6KA5 gene. This alteration results from a A to T substitution at nucleotide position 2360, causing the aspartic acid (D) at amino acid position 787 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at