15-76935570-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002902.3(RCN2):āc.295A>Gā(p.Met99Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,492 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 (ā ).
Frequency
Consequence
NM_002902.3 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 |
---|---|---|---|---|---|---|---|
RCN2 | NM_002902.3 | c.295A>G | p.Met99Val | missense_variant | 3/7 | ENST00000394885.8 | |
RCN2 | NM_001271837.2 | c.295A>G | p.Met99Val | missense_variant | 3/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RCN2 | ENST00000394885.8 | c.295A>G | p.Met99Val | missense_variant | 3/7 | 1 | NM_002902.3 | P1 | |
RCN2 | ENST00000320963.9 | c.295A>G | p.Met99Val | missense_variant | 3/8 | 5 | |||
RCN2 | ENST00000394883.3 | c.144+3585A>G | intron_variant | 5 | |||||
RCN2 | ENST00000557805.1 | c.268A>G | p.Met90Val | missense_variant, NMD_transcript_variant | 3/6 | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251160Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135768
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461492Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 727048
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 09, 2024 | The c.295A>G (p.M99V) alteration is located in exon 3 (coding exon 3) of the RCN2 gene. This alteration results from a A to G substitution at nucleotide position 295, causing the methionine (M) at amino acid position 99 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