9-124952890-G-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001144877.3(SCAI):c.1738C>A(p.His580Asn) variant causes a missense change. The variant allele was found at a frequency of 0.000148 in 1,611,314 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_001144877.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000682 AC: 17AN: 249238Hom.: 0 AF XY: 0.0000665 AC XY: 9AN XY: 135292
GnomAD4 exome AF: 0.000156 AC: 227AN: 1459112Hom.: 0 Cov.: 30 AF XY: 0.000142 AC XY: 103AN XY: 726076
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152202Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1807C>A (p.H603N) alteration is located in exon 19 (coding exon 19) of the SCAI gene. This alteration results from a C to A substitution at nucleotide position 1807, causing the histidine (H) at amino acid position 603 to be replaced by an asparagine (N). 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