chr12-27495852-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001395208.2(SMCO2):c.830C>T(p.Ala277Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000182 in 1,487,028 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 Likely benign (★).
Frequency
Consequence
NM_001395208.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMCO2 | NM_001395208.2 | c.830C>T | p.Ala277Val | missense_variant | 8/9 | ENST00000535986.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMCO2 | ENST00000535986.2 | c.830C>T | p.Ala277Val | missense_variant | 8/9 | 5 | NM_001395208.2 | ||
SMCO2 | ENST00000298876.8 | c.680C>T | p.Ala227Val | missense_variant | 7/8 | 5 | P1 | ||
SMCO2 | ENST00000698358.1 | c.443C>T | p.Ala148Val | missense_variant | 5/6 | ||||
SMCO2 | ENST00000541168.1 | n.694C>T | non_coding_transcript_exon_variant | 2/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000113 AC: 17AN: 150196Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000266 AC: 4AN: 150298Hom.: 0 AF XY: 0.0000126 AC XY: 1AN XY: 79448
GnomAD4 exome AF: 0.00000748 AC: 10AN: 1336832Hom.: 0 Cov.: 31 AF XY: 0.0000123 AC XY: 8AN XY: 652464
GnomAD4 genome AF: 0.000113 AC: 17AN: 150196Hom.: 0 Cov.: 31 AF XY: 0.000123 AC XY: 9AN XY: 73350
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 20, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at