chr11-74836039-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001098638.2(RNF169):c.1436C>T(p.Ala479Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,614,062 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_001098638.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNF169 | NM_001098638.2 | c.1436C>T | p.Ala479Val | missense_variant | 6/6 | ENST00000299563.5 | |
RNF169 | XM_011544889.4 | c.1499C>T | p.Ala500Val | missense_variant | 6/6 | ||
RNF169 | XM_047426707.1 | c.770C>T | p.Ala257Val | missense_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNF169 | ENST00000299563.5 | c.1436C>T | p.Ala479Val | missense_variant | 6/6 | 1 | NM_001098638.2 | P1 | |
XRRA1 | ENST00000530562.5 | c.*65+7311G>A | intron_variant, NMD_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152198Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249296Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135318
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461864Hom.: 0 Cov.: 33 AF XY: 0.00000825 AC XY: 6AN XY: 727232
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152198Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 02, 2023 | The c.1436C>T (p.A479V) alteration is located in exon 6 (coding exon 6) of the RNF169 gene. This alteration results from a C to T substitution at nucleotide position 1436, causing the alanine (A) at amino acid position 479 to be replaced by a valine (V). 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