3-15074192-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_022340.4(RBSN):c.1945G>T(p.Val649Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000168 in 1,610,966 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 Uncertain significance (★).
Frequency
Consequence
NM_022340.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RBSN | ENST00000253699.7 | c.1945G>T | p.Val649Phe | missense_variant | 14/14 | 1 | NM_022340.4 | ENSP00000253699.3 | ||
RBSN | ENST00000476527.6 | c.1945G>T | p.Val649Phe | missense_variant | 13/13 | 2 | ENSP00000422551.1 | |||
ENSG00000289750 | ENST00000698784.1 | n.1360G>T | non_coding_transcript_exon_variant | 8/9 | ||||||
ENSG00000289750 | ENST00000698785.1 | n.2556G>T | non_coding_transcript_exon_variant | 14/17 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000604 AC: 15AN: 248268Hom.: 0 AF XY: 0.0000447 AC XY: 6AN XY: 134112
GnomAD4 exome AF: 0.000175 AC: 255AN: 1458810Hom.: 0 Cov.: 32 AF XY: 0.000185 AC XY: 134AN XY: 725464
GnomAD4 genome AF: 0.000105 AC: 16AN: 152156Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74320
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 25, 2022 | The c.1945G>T (p.V649F) alteration is located in exon 14 (coding exon 11) of the RBSN gene. This alteration results from a G to T substitution at nucleotide position 1945, causing the valine (V) at amino acid position 649 to be replaced by a phenylalanine (F). 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