chr12-27501964-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001395208.2(SMCO2):c.875C>T(p.Thr292Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000834 in 1,546,346 control chromosomes in the GnomAD database, including 7 homozygotes. 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 Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMCO2 | NM_001395208.2 | c.875C>T | p.Thr292Ile | missense_variant | 9/9 | ENST00000535986.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMCO2 | ENST00000535986.2 | c.875C>T | p.Thr292Ile | missense_variant | 9/9 | 5 | NM_001395208.2 | ||
SMCO2 | ENST00000298876.8 | c.725C>T | p.Thr242Ile | missense_variant | 8/8 | 5 | P1 | ||
SMCO2 | ENST00000698358.1 | c.488C>T | p.Thr163Ile | missense_variant | 6/6 | ||||
SMCO2 | ENST00000541168.1 | n.739C>T | non_coding_transcript_exon_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000418 AC: 63AN: 150664Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.000148 AC: 23AN: 155182Hom.: 0 AF XY: 0.000134 AC XY: 11AN XY: 82082
GnomAD4 exome AF: 0.0000473 AC: 66AN: 1395568Hom.: 3 Cov.: 29 AF XY: 0.0000407 AC XY: 28AN XY: 688284
GnomAD4 genome ? AF: 0.000418 AC: 63AN: 150778Hom.: 4 Cov.: 32 AF XY: 0.000380 AC XY: 28AN XY: 73776
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 30, 2022 | The c.875C>T (p.T292I) alteration is located in exon 9 (coding exon 8) of the SMCO2 gene. This alteration results from a C to T substitution at nucleotide position 875, causing the threonine (T) at amino acid position 292 to be replaced by an isoleucine (I). 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