3-15074132-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_022340.4(RBSN):c.2005G>A(p.Glu669Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000116 in 1,461,870 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E669D) has been classified as Uncertain significance.
Frequency
Consequence
NM_022340.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RBSN | ENST00000253699.7 | c.2005G>A | p.Glu669Lys | missense_variant | Exon 14 of 14 | 1 | NM_022340.4 | ENSP00000253699.3 | ||
RBSN | ENST00000476527.6 | c.2005G>A | p.Glu669Lys | missense_variant | Exon 13 of 13 | 2 | ENSP00000422551.1 | |||
ENSG00000289750 | ENST00000698784.1 | n.1420G>A | non_coding_transcript_exon_variant | Exon 8 of 9 | ||||||
ENSG00000289750 | ENST00000698785.1 | n.2616G>A | non_coding_transcript_exon_variant | Exon 14 of 17 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251128Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135686
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461870Hom.: 0 Cov.: 32 AF XY: 0.0000138 AC XY: 10AN XY: 727238
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2005G>A (p.E669K) alteration is located in exon 14 (coding exon 11) of the RBSN gene. This alteration results from a G to A substitution at nucleotide position 2005, causing the glutamic acid (E) at amino acid position 669 to be replaced by a lysine (K). 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