4-42401123-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001080505.3(SHISA3):c.389C>T(p.Ser130Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000409 in 1,614,092 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_001080505.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SHISA3 | NM_001080505.3 | c.389C>T | p.Ser130Leu | missense_variant | Exon 2 of 2 | ENST00000319234.5 | NP_001073974.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152198Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000477 AC: 12AN: 251492Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135920
GnomAD4 exome AF: 0.0000315 AC: 46AN: 1461894Hom.: 0 Cov.: 33 AF XY: 0.0000248 AC XY: 18AN XY: 727248
GnomAD4 genome AF: 0.000131 AC: 20AN: 152198Hom.: 0 Cov.: 33 AF XY: 0.0000942 AC XY: 7AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.389C>T (p.S130L) alteration is located in exon 2 (coding exon 2) of the SHISA3 gene. This alteration results from a C to T substitution at nucleotide position 389, causing the serine (S) at amino acid position 130 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