rs62637569
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_014694.4(ADAMTSL2):āc.88A>Gā(p.Thr30Ala) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00217 in 1,614,182 control chromosomes in the GnomAD database, including 77 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 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 Likely benign (ā ).
Frequency
Consequence
NM_014694.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADAMTSL2 | NM_014694.4 | c.88A>G | p.Thr30Ala | missense_variant, splice_region_variant | 2/19 | ENST00000651351.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADAMTSL2 | ENST00000651351.2 | c.88A>G | p.Thr30Ala | missense_variant, splice_region_variant | 2/19 | NM_014694.4 | P1 | ||
ADAMTSL2 | ENST00000393061.7 | c.415A>G | p.Thr139Ala | missense_variant, splice_region_variant | 2/19 | 1 | |||
ADAMTSL2 | ENST00000354484.8 | c.88A>G | p.Thr30Ala | missense_variant, splice_region_variant | 2/19 | 1 | P1 | ||
ADAMTSL2 | ENST00000393060.1 | c.88A>G | p.Thr30Ala | missense_variant, splice_region_variant | 2/19 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0118 AC: 1800AN: 152226Hom.: 48 Cov.: 34
GnomAD3 exomes AF: 0.00325 AC: 815AN: 250590Hom.: 16 AF XY: 0.00253 AC XY: 343AN XY: 135576
GnomAD4 exome AF: 0.00116 AC: 1697AN: 1461838Hom.: 29 Cov.: 33 AF XY: 0.00104 AC XY: 755AN XY: 727220
GnomAD4 genome ? AF: 0.0118 AC: 1804AN: 152344Hom.: 48 Cov.: 34 AF XY: 0.0117 AC XY: 872AN XY: 74506
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | May 21, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at