rs322825
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_014390.4(SND1):c.2064T>A(p.Thr688=) 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 1,461,374 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_014390.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SND1 | NM_014390.4 | c.2064T>A | p.Thr688= | synonymous_variant | 18/24 | ENST00000354725.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SND1 | ENST00000354725.8 | c.2064T>A | p.Thr688= | synonymous_variant | 18/24 | 1 | NM_014390.4 | P1 | |
SND1 | ENST00000486037.1 | c.522T>A | p.Thr174= | synonymous_variant | 5/6 | 3 | |||
SND1 | ENST00000470463.1 | n.448T>A | non_coding_transcript_exon_variant | 3/4 | 4 | ||||
SND1 | ENST00000470723.5 | downstream_gene_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 0AN: 152098Hom.: 0 Cov.: 34 FAILED QC
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461374Hom.: 0 Cov.: 51 AF XY: 0.00000138 AC XY: 1AN XY: 727010
GnomAD4 genome ? Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 152098Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74298
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at