2-27781671-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_022128.3(RBKS):c.913G>A(p.Ala305Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000923 in 1,613,994 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 (★).
Frequency
Consequence
NM_022128.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RBKS | ENST00000302188.8 | c.913G>A | p.Ala305Thr | missense_variant | Exon 8 of 8 | 1 | NM_022128.3 | ENSP00000306817.3 | ||
RBKS | ENST00000449378.1 | n.*1840G>A | non_coding_transcript_exon_variant | Exon 9 of 9 | 1 | ENSP00000413789.1 | ||||
RBKS | ENST00000449378.1 | n.*1840G>A | 3_prime_UTR_variant | Exon 9 of 9 | 1 | ENSP00000413789.1 | ||||
MRPL33 | ENST00000448427.1 | n.42-901C>T | intron_variant | Intron 2 of 5 | 4 | ENSP00000407385.1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152124Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000159 AC: 40AN: 251306Hom.: 0 AF XY: 0.000236 AC XY: 32AN XY: 135822
GnomAD4 exome AF: 0.0000985 AC: 144AN: 1461752Hom.: 0 Cov.: 30 AF XY: 0.000135 AC XY: 98AN XY: 727182
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152242Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74436
ClinVar
Submissions by phenotype
not specified Benign:1
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