2-174404150-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_024583.5(SCRN3):c.589G>T(p.Ala197Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000062 in 1,613,624 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_024583.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152096Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251172Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135746
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461528Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 727068
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152096Hom.: 0 Cov.: 30 AF XY: 0.0000673 AC XY: 5AN XY: 74296
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.589G>T (p.A197S) alteration is located in exon 5 (coding exon 4) of the SCRN3 gene. This alteration results from a G to T substitution at nucleotide position 589, causing the alanine (A) at amino acid position 197 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