12-45924829-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_004719.3(SCAF11):c.3805C>T(p.Pro1269Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000427 in 1,614,068 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 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 Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCAF11 | NM_004719.3 | c.3805C>T | p.Pro1269Ser | missense_variant | 12/15 | ENST00000369367.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCAF11 | ENST00000369367.8 | c.3805C>T | p.Pro1269Ser | missense_variant | 12/15 | 1 | NM_004719.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000296 AC: 45AN: 152142Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251282Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135818
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1461808Hom.: 0 Cov.: 34 AF XY: 0.0000151 AC XY: 11AN XY: 727206
GnomAD4 genome AF: 0.000296 AC: 45AN: 152260Hom.: 0 Cov.: 32 AF XY: 0.000269 AC XY: 20AN XY: 74458
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 29, 2021 | The c.3805C>T (p.P1269S) alteration is located in exon 12 (coding exon 11) of the SCAF11 gene. This alteration results from a C to T substitution at nucleotide position 3805, causing the proline (P) at amino acid position 1269 to be replaced by a serine (S). 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