19-2247804-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_007165.5(SF3A2):c.653C>T(p.Pro218Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000777 in 1,609,672 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_007165.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000724 AC: 11AN: 152030Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000391 AC: 95AN: 242910Hom.: 0 AF XY: 0.000308 AC XY: 41AN XY: 133112
GnomAD4 exome AF: 0.0000782 AC: 114AN: 1457642Hom.: 0 Cov.: 33 AF XY: 0.0000717 AC XY: 52AN XY: 725336
GnomAD4 genome AF: 0.0000724 AC: 11AN: 152030Hom.: 0 Cov.: 33 AF XY: 0.0000539 AC XY: 4AN XY: 74246
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.653C>T (p.P218L) alteration is located in exon 9 (coding exon 8) of the SF3A2 gene. This alteration results from a C to T substitution at nucleotide position 653, causing the proline (P) at amino acid position 218 to be replaced by a leucine (L). 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