rs151036254
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_021228.3(SCAF1):c.352C>A(p.Arg118Arg) 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 1,461,730 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_021228.3 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SCAF1 | NM_021228.3 | c.352C>A | p.Arg118Arg | synonymous_variant | Exon 5 of 11 | ENST00000360565.8 | NP_067051.2 | |
SCAF1 | XM_011527194.4 | c.361C>A | p.Arg121Arg | synonymous_variant | Exon 5 of 11 | XP_011525496.1 | ||
SCAF1 | XM_005259122.6 | c.352C>A | p.Arg118Arg | synonymous_variant | Exon 5 of 11 | XP_005259179.1 | ||
SCAF1 | XM_017027083.3 | c.82C>A | p.Arg28Arg | synonymous_variant | Exon 2 of 8 | XP_016882572.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCAF1 | ENST00000360565.8 | c.352C>A | p.Arg118Arg | synonymous_variant | Exon 5 of 11 | 2 | NM_021228.3 | ENSP00000353769.2 | ||
SCAF1 | ENST00000595242.3 | c.356C>A | p.Ala119Glu | missense_variant | Exon 4 of 4 | 3 | ENSP00000472276.1 | |||
SCAF1 | ENST00000598359.5 | c.352C>A | p.Arg118Arg | synonymous_variant | Exon 5 of 7 | 3 | ENSP00000473210.1 | |||
SCAF1 | ENST00000601038.5 | c.*58C>A | downstream_gene_variant | 3 | ENSP00000472649.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461730Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727186
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.