chr9-133536801-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_014694.4(ADAMTSL2):c.89C>T(p.Thr30Met) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000192 in 1,614,038 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 17/22 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Consequence
NM_014694.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ADAMTSL2 | NM_014694.4 | c.89C>T | p.Thr30Met | missense_variant, splice_region_variant | 2/19 | ENST00000651351.2 | NP_055509.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ADAMTSL2 | ENST00000651351.2 | c.89C>T | p.Thr30Met | missense_variant, splice_region_variant | 2/19 | NM_014694.4 | ENSP00000498961 | P1 | ||
ADAMTSL2 | ENST00000393061.7 | c.416C>T | p.Thr139Met | missense_variant, splice_region_variant | 2/19 | 1 | ENSP00000376781 | |||
ADAMTSL2 | ENST00000354484.8 | c.89C>T | p.Thr30Met | missense_variant, splice_region_variant | 2/19 | 1 | ENSP00000346478 | P1 | ||
ADAMTSL2 | ENST00000393060.1 | c.89C>T | p.Thr30Met | missense_variant, splice_region_variant | 2/19 | 1 | ENSP00000376780 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152208Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000359 AC: 9AN: 250528Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135548
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1461830Hom.: 0 Cov.: 33 AF XY: 0.0000193 AC XY: 14AN XY: 727214
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152208Hom.: 0 Cov.: 34 AF XY: 0.0000403 AC XY: 3AN XY: 74360
ClinVar
Submissions by phenotype
ADAMTSL2-related disorder Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 07, 2024 | The ADAMTSL2 c.89C>T variant is predicted to result in the amino acid substitution p.Thr30Met. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.014% of alleles in individuals of Latino descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at