12-45925071-G-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_004719.3(SCAF11):c.3563C>G(p.Ser1188Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000555 in 1,442,680 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004719.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCAF11 | ENST00000369367.8 | c.3563C>G | p.Ser1188Cys | missense_variant | Exon 12 of 15 | 1 | NM_004719.3 | ENSP00000358374.3 | ||
SCAF11 | ENST00000549162.5 | c.2987C>G | p.Ser996Cys | missense_variant | Exon 6 of 9 | 1 | ENSP00000448864.1 | |||
SCAF11 | ENST00000465950.5 | c.2618C>G | p.Ser873Cys | missense_variant | Exon 2 of 5 | 1 | ENSP00000449812.1 | |||
SCAF11 | ENST00000547950.1 | n.573C>G | non_coding_transcript_exon_variant | Exon 2 of 2 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000209 AC: 5AN: 239702Hom.: 0 AF XY: 0.0000153 AC XY: 2AN XY: 130316
GnomAD4 exome AF: 0.00000555 AC: 8AN: 1442680Hom.: 0 Cov.: 33 AF XY: 0.00000140 AC XY: 1AN XY: 715496
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3563C>G (p.S1188C) alteration is located in exon 12 (coding exon 11) of the SCAF11 gene. This alteration results from a C to G substitution at nucleotide position 3563, causing the serine (S) at amino acid position 1188 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at