chr15-83773520-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_207517.3(ADAMTSL3):c.190-3T>C variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0658 in 1,612,916 control chromosomes in the GnomAD database, including 4,178 homozygotes. In-silico tool predicts 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 Benign (★).
Frequency
Consequence
NM_207517.3 splice_region, splice_polypyrimidine_tract, intron
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 |
---|---|---|---|---|---|---|---|
ADAMTSL3 | NM_207517.3 | c.190-3T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000286744.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADAMTSL3 | ENST00000286744.10 | c.190-3T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_207517.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0630 AC: 9581AN: 151970Hom.: 386 Cov.: 32
GnomAD3 exomes AF: 0.0698 AC: 17508AN: 250854Hom.: 803 AF XY: 0.0707 AC XY: 9583AN XY: 135582
GnomAD4 exome AF: 0.0661 AC: 96529AN: 1460826Hom.: 3789 Cov.: 33 AF XY: 0.0663 AC XY: 48161AN XY: 726762
GnomAD4 genome ? AF: 0.0631 AC: 9591AN: 152090Hom.: 389 Cov.: 32 AF XY: 0.0645 AC XY: 4797AN XY: 74348
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 10, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at