16-85678618-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_016095.3(GINS2):c.354G>A(p.Lys118Lys) 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 1,461,628 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_016095.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GINS2 | ENST00000253462.8 | c.354G>A | p.Lys118Lys | synonymous_variant | Exon 4 of 5 | 1 | NM_016095.3 | ENSP00000253462.3 | ||
GINS2 | ENST00000595355.5 | c.159G>A | p.Lys53Lys | synonymous_variant | Exon 4 of 4 | 3 | ENSP00000470984.1 | |||
GINS2 | ENST00000596233.1 | c.*5G>A | downstream_gene_variant | 3 | ENSP00000469346.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461628Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727098
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at