chr12-27470717-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001395208.2(SMCO2):c.86A>G(p.Asn29Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000548 in 1,551,096 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
Genome browser will be placed here
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.86A>G | p.Asn29Ser | missense_variant | 2/9 | ENST00000535986.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMCO2 | ENST00000535986.2 | c.86A>G | p.Asn29Ser | missense_variant | 2/9 | 5 | NM_001395208.2 | ||
SMCO2 | ENST00000298876.8 | c.86A>G | p.Asn29Ser | missense_variant | 2/8 | 5 | P1 | ||
SMCO2 | ENST00000698358.1 | c.-3-4069A>G | intron_variant | ||||||
SMCO2 | ENST00000543991.1 | n.96A>G | non_coding_transcript_exon_variant | 1/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000128 AC: 2AN: 156438Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 82790
GnomAD4 exome AF: 0.0000572 AC: 80AN: 1398912Hom.: 0 Cov.: 31 AF XY: 0.0000638 AC XY: 44AN XY: 689964
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 01, 2021 | The c.86A>G (p.N29S) 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 86, causing the asparagine (N) at amino acid position 29 to be replaced by a serine (S). 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