12-45924772-G-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_004719.3(SCAF11):c.3862C>A(p.Gln1288Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000468 in 1,516,512 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_004719.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000135 AC: 2AN: 148530Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250314Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135278
GnomAD4 exome AF: 0.0000504 AC: 69AN: 1367982Hom.: 0 Cov.: 50 AF XY: 0.0000512 AC XY: 35AN XY: 683952
GnomAD4 genome AF: 0.0000135 AC: 2AN: 148530Hom.: 0 Cov.: 32 AF XY: 0.0000138 AC XY: 1AN XY: 72308
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3862C>A (p.Q1288K) alteration is located in exon 12 (coding exon 11) of the SCAF11 gene. This alteration results from a C to A substitution at nucleotide position 3862, causing the glutamine (Q) at amino acid position 1288 to be replaced by a lysine (K). 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