7-129456443-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_020704.3(STRIP2):c.839C>T(p.Thr280Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,613,800 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_020704.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
STRIP2 | ENST00000249344.7 | c.839C>T | p.Thr280Ile | missense_variant | Exon 9 of 21 | 1 | NM_020704.3 | ENSP00000249344.2 | ||
STRIP2 | ENST00000435494.2 | c.839C>T | p.Thr280Ile | missense_variant | Exon 9 of 20 | 1 | ENSP00000392393.2 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151998Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251030Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135686
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461802Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 727208
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151998Hom.: 0 Cov.: 30 AF XY: 0.0000135 AC XY: 1AN XY: 74224
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.839C>T (p.T280I) alteration is located in exon 9 (coding exon 9) of the STRIP2 gene. This alteration results from a C to T substitution at nucleotide position 839, causing the threonine (T) at amino acid position 280 to be replaced by an isoleucine (I). 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