chr12-27470693-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001395208.2(SMCO2):āc.62A>Gā(p.Gln21Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000011 in 1,551,192 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 (ā ).
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.62A>G | p.Gln21Arg | missense_variant | 2/9 | ENST00000535986.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMCO2 | ENST00000535986.2 | c.62A>G | p.Gln21Arg | missense_variant | 2/9 | 5 | NM_001395208.2 | ||
SMCO2 | ENST00000298876.8 | c.62A>G | p.Gln21Arg | missense_variant | 2/8 | 5 | P1 | ||
SMCO2 | ENST00000698358.1 | c.-3-4093A>G | intron_variant | ||||||
SMCO2 | ENST00000543991.1 | n.72A>G | non_coding_transcript_exon_variant | 1/2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000128 AC: 2AN: 156286Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 82776
GnomAD4 exome AF: 0.00000929 AC: 13AN: 1398982Hom.: 0 Cov.: 31 AF XY: 0.00000725 AC XY: 5AN XY: 690008
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152210Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 30, 2023 | The c.62A>G (p.Q21R) alteration is located in exon 2 (coding exon 1) of the SMCO2 gene. This alteration results from a A to G substitution at nucleotide position 62, causing the glutamine (Q) at amino acid position 21 to be replaced by an arginine (R). 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