2-86604177-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_005667.4(RNF103):c.1724C>T(p.Ala575Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,414 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/23 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005667.4 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RNF103 | NM_005667.4 | c.1724C>T | p.Ala575Val | missense_variant | 4/4 | ENST00000237455.5 | NP_005658.1 | |
RNF103-CHMP3 | NM_001198954.1 | c.132+16153C>T | intron_variant | NP_001185883.1 | ||||
CHMP3-AS1 | NR_183900.1 | n.254-12999G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RNF103 | ENST00000237455.5 | c.1724C>T | p.Ala575Val | missense_variant | 4/4 | 1 | NM_005667.4 | ENSP00000237455 | P1 | |
CHMP3-AS1 | ENST00000439077.1 | n.249-12999G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461414Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727034
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 15, 2023 | The c.1724C>T (p.A575V) alteration is located in exon 4 (coding exon 4) of the RNF103 gene. This alteration results from a C to T substitution at nucleotide position 1724, causing the alanine (A) at amino acid position 575 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