chr12-27494351-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001395208.2(SMCO2):āc.652C>Gā(p.Leu218Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000125 in 1,522,724 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001395208.2 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 |
---|---|---|---|---|---|---|---|
SMCO2 | NM_001395208.2 | c.652C>G | p.Leu218Val | missense_variant | 7/9 | ENST00000535986.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMCO2 | ENST00000535986.2 | c.652C>G | p.Leu218Val | missense_variant | 7/9 | 5 | NM_001395208.2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 151874Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000834 AC: 11AN: 131934Hom.: 0 AF XY: 0.0000428 AC XY: 3AN XY: 70126
GnomAD4 exome AF: 0.0000109 AC: 15AN: 1370850Hom.: 0 Cov.: 26 AF XY: 0.00000592 AC XY: 4AN XY: 675740
GnomAD4 genome AF: 0.0000263 AC: 4AN: 151874Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74212
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 18, 2022 | The c.652C>G (p.L218V) alteration is located in exon 7 (coding exon 6) of the SMCO2 gene. This alteration results from a C to G substitution at nucleotide position 652, causing the leucine (L) at amino acid position 218 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