12-27502075-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001395208.2(SMCO2):c.986G>A(p.Arg329Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000647 in 1,544,674 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001395208.2 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 |
---|---|---|---|---|---|---|---|
SMCO2 | NM_001395208.2 | c.986G>A | p.Arg329Lys | missense_variant | 9/9 | ENST00000535986.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMCO2 | ENST00000535986.2 | c.986G>A | p.Arg329Lys | missense_variant | 9/9 | 5 | NM_001395208.2 | ||
SMCO2 | ENST00000298876.8 | c.836G>A | p.Arg279Lys | missense_variant | 8/8 | 5 | P1 | ||
SMCO2 | ENST00000698358.1 | c.599G>A | p.Arg200Lys | missense_variant | 6/6 | ||||
SMCO2 | ENST00000541168.1 | n.850G>A | non_coding_transcript_exon_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000665 AC: 1AN: 150428Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000653 AC: 1AN: 153088Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 81072
GnomAD4 exome AF: 0.00000646 AC: 9AN: 1394246Hom.: 0 Cov.: 31 AF XY: 0.00000291 AC XY: 2AN XY: 687656
GnomAD4 genome ? AF: 0.00000665 AC: 1AN: 150428Hom.: 0 Cov.: 32 AF XY: 0.0000136 AC XY: 1AN XY: 73478
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 02, 2023 | The c.986G>A (p.R329K) alteration is located in exon 9 (coding exon 8) of the SMCO2 gene. This alteration results from a G to A substitution at nucleotide position 986, causing the arginine (R) at amino acid position 329 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