22-50523635-C-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_005138.3(SCO2):c.777G>C(p.Ala259=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,410 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. A259A) has been classified as Likely benign.
Frequency
Consequence
NM_005138.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCO2 | NM_005138.3 | c.777G>C | p.Ala259= | synonymous_variant | 2/2 | ENST00000395693.8 | |
NCAPH2 | NM_152299.4 | c.*260C>G | 3_prime_UTR_variant | 20/20 | ENST00000420993.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCO2 | ENST00000395693.8 | c.777G>C | p.Ala259= | synonymous_variant | 2/2 | 1 | NM_005138.3 | P1 | |
NCAPH2 | ENST00000420993.7 | c.*260C>G | 3_prime_UTR_variant | 20/20 | 1 | NM_152299.4 | P4 |
Frequencies
GnomAD3 genomes ? Cov.: 34
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251170Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135846
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461410Hom.: 0 Cov.: 35 AF XY: 0.00 AC XY: 0AN XY: 727020
GnomAD4 genome ? Cov.: 34
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 17, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at