chr12-27472786-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.145G>A(p.Glu49Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000129 in 1,550,336 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 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.145G>A | p.Glu49Lys | missense_variant | 3/9 | ENST00000535986.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMCO2 | ENST00000535986.2 | c.145G>A | p.Glu49Lys | missense_variant | 3/9 | 5 | NM_001395208.2 | ||
SMCO2 | ENST00000298876.8 | c.145G>A | p.Glu49Lys | missense_variant | 3/8 | 5 | P1 | ||
SMCO2 | ENST00000698358.1 | c.-3-2000G>A | intron_variant | ||||||
SMCO2 | ENST00000543991.1 | n.155G>A | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152114Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000641 AC: 1AN: 155946Hom.: 0 AF XY: 0.0000121 AC XY: 1AN XY: 82658
GnomAD4 exome AF: 0.00000715 AC: 10AN: 1398222Hom.: 0 Cov.: 30 AF XY: 0.0000102 AC XY: 7AN XY: 689646
GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152114Hom.: 0 Cov.: 33 AF XY: 0.0000807 AC XY: 6AN XY: 74314
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 12, 2021 | The c.145G>A (p.E49K) alteration is located in exon 3 (coding exon 2) of the SMCO2 gene. This alteration results from a G to A substitution at nucleotide position 145, causing the glutamic acid (E) at amino acid position 49 to be replaced by a lysine (K). 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