chr1-232399189-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_020808.5(SIPA1L2):c.5107G>A(p.Ala1703Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000868 in 1,613,750 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020808.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 151886Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249494Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135354
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461864Hom.: 0 Cov.: 30 AF XY: 0.00000688 AC XY: 5AN XY: 727242
GnomAD4 genome AF: 0.0000329 AC: 5AN: 151886Hom.: 0 Cov.: 31 AF XY: 0.0000539 AC XY: 4AN XY: 74170
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.5107G>A (p.A1703T) alteration is located in exon 21 (coding exon 21) of the SIPA1L2 gene. This alteration results from a G to A substitution at nucleotide position 5107, causing the alanine (A) at amino acid position 1703 to be replaced by a threonine (T). 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