chr12-27501949-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001395208.2(SMCO2):c.860T>C(p.Met287Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000079 in 1,392,800 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 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.860T>C | p.Met287Thr | missense_variant | 9/9 | ENST00000535986.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMCO2 | ENST00000535986.2 | c.860T>C | p.Met287Thr | missense_variant | 9/9 | 5 | NM_001395208.2 | ||
SMCO2 | ENST00000298876.8 | c.710T>C | p.Met237Thr | missense_variant | 8/8 | 5 | P1 | ||
SMCO2 | ENST00000698358.1 | c.473T>C | p.Met158Thr | missense_variant | 6/6 | ||||
SMCO2 | ENST00000541168.1 | n.724T>C | non_coding_transcript_exon_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000790 AC: 11AN: 1392800Hom.: 0 Cov.: 29 AF XY: 0.00000582 AC XY: 4AN XY: 686796
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 15, 2023 | The c.860T>C (p.M287T) alteration is located in exon 9 (coding exon 8) of the SMCO2 gene. This alteration results from a T to C substitution at nucleotide position 860, causing the methionine (M) at amino acid position 287 to be replaced by a threonine (T). 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