X-84187888-G-A
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Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_014496.5(RPS6KA6):c.12C>T(p.Phe4=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000418 in 1,196,553 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000018 ( 0 hom., 1 hem., cov: 22)
Exomes 𝑓: 0.0000028 ( 0 hom. 1 hem. )
Consequence
RPS6KA6
NM_014496.5 synonymous
NM_014496.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.154
Genes affected
RPS6KA6 (HGNC:10435): (ribosomal protein S6 kinase A6) This gene encodes a member of ribosomal S6 kinase family, serine-threonine protein kinases which are regulated by growth factors. The encoded protein may be distinct from other members of this family, however, as studies suggest it is not growth factor dependent and may not participate in the same signaling pathways. [provided by RefSeq, Jan 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.65).
BP6
Variant X-84187888-G-A is Benign according to our data. Variant chrX-84187888-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2660998.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.154 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPS6KA6 | NM_014496.5 | c.12C>T | p.Phe4= | synonymous_variant | 1/22 | ENST00000262752.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPS6KA6 | ENST00000262752.5 | c.12C>T | p.Phe4= | synonymous_variant | 1/22 | 1 | NM_014496.5 | P1 | |
RPS6KA6 | ENST00000460730.1 | n.11C>T | non_coding_transcript_exon_variant | 1/6 | 3 | ||||
RPS6KA6 | ENST00000699863.1 | n.84+386C>T | intron_variant, non_coding_transcript_variant | ||||||
RPS6KA6 | ENST00000699864.1 | n.110+18359C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000182 AC: 2AN: 109657Hom.: 0 Cov.: 22 AF XY: 0.0000309 AC XY: 1AN XY: 32315
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GnomAD3 exomes AF: 0.0000182 AC: 3AN: 164741Hom.: 0 AF XY: 0.0000188 AC XY: 1AN XY: 53315
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GnomAD4 exome AF: 0.00000276 AC: 3AN: 1086896Hom.: 0 Cov.: 30 AF XY: 0.00000282 AC XY: 1AN XY: 354684
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GnomAD4 genome AF: 0.0000182 AC: 2AN: 109657Hom.: 0 Cov.: 22 AF XY: 0.0000309 AC XY: 1AN XY: 32315
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2022 | RPS6KA6: BP4, BP7 - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at