chr9-18533259-A-G
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_001040272.6(ADAMTSL1):c.204A>G(p.Gly68=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00229 in 1,606,928 control chromosomes in the GnomAD database, including 81 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.013 ( 51 hom., cov: 32)
Exomes 𝑓: 0.0012 ( 30 hom. )
Consequence
ADAMTSL1
NM_001040272.6 synonymous
NM_001040272.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.44
Genes affected
ADAMTSL1 (HGNC:14632): (ADAMTS like 1) This gene encodes a secreted protein and member of the ADAMTS (a disintegrin and metalloproteinase with thrombospondin motif) family. This protein lacks the metalloproteinase and disintegrin-like domains, which are typical of the ADAMTS family, but contains other ADAMTS domains, including the thrombospondin type 1 motif. This protein may have important functions in the extracellular matrix. Alternative splicing results in multiple transcript variants encoding distinct proteins. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
BP6
?
Variant 9-18533259-A-G is Benign according to our data. Variant chr9-18533259-A-G is described in ClinVar as [Benign]. Clinvar id is 771427.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=1.44 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0127 (1941/152242) while in subpopulation AFR AF= 0.0444 (1845/41558). AF 95% confidence interval is 0.0427. There are 51 homozygotes in gnomad4. There are 915 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 51 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADAMTSL1 | NM_001040272.6 | c.204A>G | p.Gly68= | synonymous_variant | 3/29 | ENST00000380548.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADAMTSL1 | ENST00000380548.9 | c.204A>G | p.Gly68= | synonymous_variant | 3/29 | 5 | NM_001040272.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0128 AC: 1942AN: 152124Hom.: 51 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
1942
AN:
152124
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00303 AC: 745AN: 246250Hom.: 17 AF XY: 0.00224 AC XY: 298AN XY: 133232
GnomAD3 exomes
AF:
AC:
745
AN:
246250
Hom.:
AF XY:
AC XY:
298
AN XY:
133232
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00120 AC: 1742AN: 1454686Hom.: 30 Cov.: 29 AF XY: 0.00107 AC XY: 772AN XY: 723738
GnomAD4 exome
AF:
AC:
1742
AN:
1454686
Hom.:
Cov.:
29
AF XY:
AC XY:
772
AN XY:
723738
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.0127 AC: 1941AN: 152242Hom.: 51 Cov.: 32 AF XY: 0.0123 AC XY: 915AN XY: 74426
GnomAD4 genome
?
AF:
AC:
1941
AN:
152242
Hom.:
Cov.:
32
AF XY:
AC XY:
915
AN XY:
74426
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
3
AN:
3470
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Name
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