2-101282042-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_173647.4(RNF149):c.976G>A(p.Val326Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000057 in 1,613,728 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_173647.4 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 |
---|---|---|---|---|---|---|---|---|---|---|
RNF149 | ENST00000295317.4 | c.976G>A | p.Val326Ile | missense_variant | 6/7 | 1 | NM_173647.4 | ENSP00000295317.3 | ||
RNF149 | ENST00000424632.5 | n.976G>A | non_coding_transcript_exon_variant | 6/8 | 2 | ENSP00000399090.1 | ||||
RNF149 | ENST00000463726.1 | n.439G>A | non_coding_transcript_exon_variant | 2/2 | 4 | |||||
RNF149 | ENST00000490553.1 | n.43G>A | non_coding_transcript_exon_variant | 2/2 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 152052Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000716 AC: 18AN: 251284Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135816
GnomAD4 exome AF: 0.0000588 AC: 86AN: 1461676Hom.: 0 Cov.: 33 AF XY: 0.0000660 AC XY: 48AN XY: 727154
GnomAD4 genome AF: 0.0000395 AC: 6AN: 152052Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74246
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 05, 2023 | The c.976G>A (p.V326I) alteration is located in exon 6 (coding exon 6) of the RNF149 gene. This alteration results from a G to A substitution at nucleotide position 976, causing the valine (V) at amino acid position 326 to be replaced by an isoleucine (I). 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