15-83913372-G-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_207517.3(ADAMTSL3):c.1981G>T(p.Val661Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.557 in 1,611,870 control chromosomes in the GnomAD database, including 255,803 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_207517.3 missense
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.1981G>T | p.Val661Leu | missense_variant | 16/30 | ENST00000286744.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADAMTSL3 | ENST00000286744.10 | c.1981G>T | p.Val661Leu | missense_variant | 16/30 | 1 | NM_207517.3 | P1 | |
ADAMTSL3 | ENST00000567476.1 | c.1981G>T | p.Val661Leu | missense_variant | 16/30 | 1 | |||
ADAMTSL3 | ENST00000561483.5 | n.2196G>T | non_coding_transcript_exon_variant | 16/27 | 5 |
Frequencies
GnomAD3 genomes AF: 0.627 AC: 95235AN: 151922Hom.: 30953 Cov.: 31
GnomAD3 exomes AF: 0.607 AC: 149827AN: 246792Hom.: 47183 AF XY: 0.595 AC XY: 79447AN XY: 133544
GnomAD4 exome AF: 0.550 AC: 802953AN: 1459830Hom.: 224802 Cov.: 53 AF XY: 0.550 AC XY: 399327AN XY: 726160
GnomAD4 genome AF: 0.627 AC: 95345AN: 152040Hom.: 31001 Cov.: 31 AF XY: 0.628 AC XY: 46703AN XY: 74322
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