chr12-27488534-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001395208.2(SMCO2):c.587G>A(p.Gly196Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000949 in 1,539,190 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMCO2 | NM_001395208.2 | c.587G>A | p.Gly196Glu | missense_variant | 6/9 | ENST00000535986.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMCO2 | ENST00000535986.2 | c.587G>A | p.Gly196Glu | missense_variant | 6/9 | 5 | NM_001395208.2 | ||
SMCO2 | ENST00000298876.8 | c.437G>A | p.Gly146Glu | missense_variant | 5/8 | 5 | P1 | ||
SMCO2 | ENST00000698358.1 | c.200G>A | p.Gly67Glu | missense_variant | 3/6 | ||||
SMCO2 | ENST00000538647.1 | n.169-7146G>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000519 AC: 79AN: 152130Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000108 AC: 16AN: 147688Hom.: 0 AF XY: 0.000141 AC XY: 11AN XY: 78224
GnomAD4 exome AF: 0.0000483 AC: 67AN: 1386942Hom.: 0 Cov.: 30 AF XY: 0.0000380 AC XY: 26AN XY: 683416
GnomAD4 genome ? AF: 0.000519 AC: 79AN: 152248Hom.: 0 Cov.: 32 AF XY: 0.000403 AC XY: 30AN XY: 74456
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 30, 2022 | The c.587G>A (p.G196E) alteration is located in exon 6 (coding exon 5) of the SMCO2 gene. This alteration results from a G to A substitution at nucleotide position 587, causing the glycine (G) at amino acid position 196 to be replaced by a glutamic acid (E). 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