GeneBe

rs11301352

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_207517.3(ADAMTSL3):​c.364-138_364-132delAAAAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000223 in 403,488 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)
Exomes 𝑓: 0.000022 ( 0 hom. )

Consequence

ADAMTSL3
NM_207517.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.83

Publications

0 publications found
Variant links:
Genes affected
ADAMTSL3 (HGNC:14633): (ADAMTS like 3) Predicted to be involved in extracellular matrix organization. Located in intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_207517.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
ADAMTSL3
NM_207517.3
MANE Select
c.364-138_364-132delAAAAAAA
intron
N/ANP_997400.2P82987-1
ADAMTSL3
NM_001301110.2
c.364-138_364-132delAAAAAAA
intron
N/ANP_001288039.1P82987-2

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
ADAMTSL3
ENST00000286744.10
TSL:1 MANE Select
c.364-149_364-143delAAAAAAA
intron
N/AENSP00000286744.5P82987-1
ADAMTSL3
ENST00000567476.1
TSL:1
c.364-149_364-143delAAAAAAA
intron
N/AENSP00000456313.1P82987-2
ADAMTSL3
ENST00000963409.1
c.364-149_364-143delAAAAAAA
intron
N/AENSP00000633468.1

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
0.0000223
AC:
9
AN:
403488
Hom.:
0
AF XY:
0.00000946
AC XY:
2
AN XY:
211436
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
0.00
AC:
0
AN:
11420
American (AMR)
AF:
0.00
AC:
0
AN:
17478
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
12350
East Asian (EAS)
AF:
0.00
AC:
0
AN:
28806
South Asian (SAS)
AF:
0.0000533
AC:
2
AN:
37492
European-Finnish (FIN)
AF:
0.000109
AC:
3
AN:
27498
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
1776
European-Non Finnish (NFE)
AF:
0.0000164
AC:
4
AN:
243274
Other (OTH)
AF:
0.00
AC:
0
AN:
23394
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.242
Heterozygous variant carriers
0
2
3
5
6
8
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
1.8

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs11301352; hg19: chr15-84488413; API