chr11-74789679-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001098638.2(RNF169):c.556G>A(p.Glu186Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000905 in 1,602,422 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. E186G) has been classified 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 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNF169 | NM_001098638.2 | c.556G>A | p.Glu186Lys | missense_variant | 2/6 | ENST00000299563.5 | |
RNF169 | XM_011544889.4 | c.619G>A | p.Glu207Lys | missense_variant | 2/6 | ||
RNF169 | XM_047426707.1 | c.-111G>A | 5_prime_UTR_variant | 2/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNF169 | ENST00000299563.5 | c.556G>A | p.Glu186Lys | missense_variant | 2/6 | 1 | NM_001098638.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152168Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000241 AC: 6AN: 249064Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135158
GnomAD4 exome AF: 0.0000979 AC: 142AN: 1450254Hom.: 0 Cov.: 26 AF XY: 0.000112 AC XY: 81AN XY: 722356
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152168Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74320
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 17, 2021 | The c.556G>A (p.E186K) alteration is located in exon 2 (coding exon 2) of the RNF169 gene. This alteration results from a G to A substitution at nucleotide position 556, causing the glutamic acid (E) at amino acid position 186 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