rs965442864
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_001286188.1(SCAF8):c.72C>T(p.Ser24Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000567 in 1,322,030 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 Uncertain significance (★).
Frequency
Consequence
NM_001286188.1 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 |
---|---|---|---|---|---|---|---|---|---|---|
SCAF8 | ENST00000367178 | c.-407C>T | 5_prime_UTR_variant | Exon 1 of 20 | 2 | NM_014892.5 | ENSP00000356146.3 | |||
SCAF8 | ENST00000417268.3 | c.72C>T | p.Ser24Ser | synonymous_variant | Exon 1 of 21 | 2 | ENSP00000413098.2 | |||
SCAF8 | ENST00000367186.7 | c.72C>T | p.Ser24Ser | synonymous_variant | Exon 1 of 22 | 2 | ENSP00000356154.4 | |||
SCAF8 | ENST00000461219.5 | n.117C>T | non_coding_transcript_exon_variant | Exon 1 of 6 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 151760Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000156 AC: 1AN: 6402Hom.: 0 AF XY: 0.000282 AC XY: 1AN XY: 3542
GnomAD4 exome AF: 0.0000513 AC: 60AN: 1170164Hom.: 0 Cov.: 30 AF XY: 0.0000617 AC XY: 35AN XY: 567198
GnomAD4 genome AF: 0.0000988 AC: 15AN: 151866Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74210
ClinVar
Submissions by phenotype
not specified Uncertain:1
Variant summary: SCAF8 c.-407C>T is located in the untranslated mRNA region upstream of the initiation codon. The variant allele was found at a frequency of 0.00016 in 6402 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.-407C>T in individuals affected with SCAF8-Related Disorders and no experimental evidence demonstrating its impact on protein function have been reported. No submitters have cited clinical-significance assessments for this variant to ClinVar. Based on the evidence outlined above, the variant was classified as uncertain significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at