chr2-27847066-C-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_022128.3(RBKS):c.325G>T(p.Ala109Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000747 in 1,606,914 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_022128.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RBKS | ENST00000302188.8 | c.325G>T | p.Ala109Ser | missense_variant | Exon 4 of 8 | 1 | NM_022128.3 | ENSP00000306817.3 | ||
RBKS | ENST00000449378.1 | n.*1252G>T | non_coding_transcript_exon_variant | Exon 5 of 9 | 1 | ENSP00000413789.1 | ||||
RBKS | ENST00000449378.1 | n.*1252G>T | 3_prime_UTR_variant | Exon 5 of 9 | 1 | ENSP00000413789.1 | ||||
MRPL33 | ENST00000448427.1 | n.165-47467C>A | intron_variant | Intron 3 of 5 | 4 | ENSP00000407385.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152128Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000756 AC: 11AN: 1454786Hom.: 0 Cov.: 27 AF XY: 0.00000690 AC XY: 5AN XY: 724202
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152128Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74294
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.325G>T (p.A109S) alteration is located in exon 4 (coding exon 4) of the RBKS gene. This alteration results from a G to T substitution at nucleotide position 325, causing the alanine (A) at amino acid position 109 to be replaced by a serine (S). 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