rs950169
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000286744.10(ADAMTSL3):c.4979C>T(p.Thr1660Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 1,601,146 control chromosomes in the GnomAD database, including 51,901 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 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
ENST00000286744.10 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ADAMTSL3 | NM_207517.3 | c.4979C>T | p.Thr1660Ile | missense_variant | 30/30 | ENST00000286744.10 | NP_997400.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ADAMTSL3 | ENST00000286744.10 | c.4979C>T | p.Thr1660Ile | missense_variant | 30/30 | 1 | NM_207517.3 | ENSP00000286744 | P1 | |
ADAMTSL3 | ENST00000567476.1 | c.4987-54C>T | intron_variant | 1 | ENSP00000456313 |
Frequencies
GnomAD3 genomes AF: 0.193 AC: 29376AN: 152098Hom.: 3670 Cov.: 33
GnomAD3 exomes AF: 0.222 AC: 53411AN: 240738Hom.: 6762 AF XY: 0.230 AC XY: 29949AN XY: 129938
GnomAD4 exome AF: 0.251 AC: 363272AN: 1448930Hom.: 48231 Cov.: 32 AF XY: 0.252 AC XY: 181539AN XY: 720624
GnomAD4 genome AF: 0.193 AC: 29373AN: 152216Hom.: 3670 Cov.: 33 AF XY: 0.192 AC XY: 14316AN XY: 74422
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 10, 2018 | This variant is associated with the following publications: (PMID: 19197363, 21239144) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at