12-45926560-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_004719.3(SCAF11):c.3141G>T(p.Trp1047Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00000124 in 1,612,234 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. W1047L) has been classified as Uncertain significance.
Frequency
Consequence
NM_004719.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCAF11 | NM_004719.3 | c.3141G>T | p.Trp1047Cys | missense_variant | 11/15 | ENST00000369367.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCAF11 | ENST00000369367.8 | c.3141G>T | p.Trp1047Cys | missense_variant | 11/15 | 1 | NM_004719.3 | P1 | |
SCAF11 | ENST00000549162.5 | c.2565G>T | p.Trp855Cys | missense_variant | 5/9 | 1 | |||
SCAF11 | ENST00000465950.5 | c.2196G>T | p.Trp732Cys | missense_variant | 1/5 | 1 | |||
SCAF11 | ENST00000547950.1 | n.151G>T | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152146Hom.: 0 Cov.: 32
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460088Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 726368
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152146Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74318
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 09, 2023 | The c.3141G>T (p.W1047C) alteration is located in exon 11 (coding exon 10) of the SCAF11 gene. This alteration results from a G to T substitution at nucleotide position 3141, causing the tryptophan (W) at amino acid position 1047 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