rs777512904
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014694.4(ADAMTSL2):c.73G>A(p.Val25Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,802 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 34)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
ADAMTSL2
NM_014694.4 missense
NM_014694.4 missense
Scores
1
17
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.520
Genes affected
ADAMTSL2 (HGNC:14631): (ADAMTS like 2) This gene encodes a member of the ADAMTS (a disintegrin and metalloproteinase with thrombospondin motifs) and ADAMTS-like protein family. Members of the family share several distinct protein modules, including a propeptide region, a metalloproteinase domain, a disintegrin-like domain, and a thrombospondin type 1 (TS) motif. Individual members of this family differ in the number of C-terminal TS motifs, and some have unique C-terminal domains. The protein encoded by this gene lacks the protease domain, and is therefore of a member of the the ADAMTS-like protein subfamily. It is a secreted glycoprotein that binds the cell surface and extracellular matrix; it also interacts with latent transforming growth factor beta binding protein 1. Mutations in this gene have been associated with geleophysic dysplasia. [provided by RefSeq, Feb 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.055009633).
Transcripts
RefSeq
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| ADAMTSL2 | ENST00000651351.2 | c.73G>A | p.Val25Met | missense_variant | Exon 2 of 19 | NM_014694.4 | ENSP00000498961.2 | |||
| ADAMTSL2 | ENST00000393061.7 | c.400G>A | p.Val134Met | missense_variant | Exon 2 of 19 | 1 | ENSP00000376781.3 | |||
| ADAMTSL2 | ENST00000354484.8 | c.73G>A | p.Val25Met | missense_variant | Exon 2 of 19 | 1 | ENSP00000346478.4 | |||
| ADAMTSL2 | ENST00000393060.1 | c.73G>A | p.Val25Met | missense_variant | Exon 2 of 19 | 1 | ENSP00000376780.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
34
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461802Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 727200
GnomAD4 exome
AF:
AC:
1
AN:
1461802
Hom.:
Cov.:
33
AF XY:
AC XY:
0
AN XY:
727200
Gnomad4 AFR exome
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GnomAD4 genome
GnomAD4 genome
Cov.:
34
Bravo
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
.;T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Uncertain
D;D;D
Sift4G
Benign
T;T;T
Polyphen
B;.;B
Vest4
MutPred
Gain of phosphorylation at T30 (P = 0.1005);.;Gain of phosphorylation at T30 (P = 0.1005);
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at