chr8-26656655-G-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_001197293.3(DPYSL2):c.*949G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0136 in 152,222 control chromosomes in the GnomAD database, including 53 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.014 ( 53 hom., cov: 31)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
DPYSL2
NM_001197293.3 3_prime_UTR
NM_001197293.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.38
Publications
1 publications found
Genes affected
DPYSL2 (HGNC:3014): (dihydropyrimidinase like 2) This gene encodes a member of the collapsin response mediator protein family. Collapsin response mediator proteins form homo- and hetero-tetramers and facilitate neuron guidance, growth and polarity. The encoded protein promotes microtubule assembly and is required for Sema3A-mediated growth cone collapse, and also plays a role in synaptic signaling through interactions with calcium channels. This gene has been implicated in multiple neurological disorders, and hyperphosphorylation of the encoded protein may play a key role in the development of Alzheimer's disease. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Sep 2011]
DPYSL2 Gene-Disease associations (from GenCC):
- schizophreniaInheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BS1
Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0136 (2069/152222) while in subpopulation AFR AF = 0.046 (1909/41534). AF 95% confidence interval is 0.0442. There are 53 homozygotes in GnomAd4. There are 1001 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
BS2
High Homozygotes in GnomAd4 at 53 Unknown gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DPYSL2 | NM_001197293.3 | c.*949G>A | 3_prime_UTR_variant | Exon 14 of 14 | ENST00000521913.7 | NP_001184222.1 | ||
DPYSL2 | NM_001386.6 | c.*949G>A | 3_prime_UTR_variant | Exon 14 of 14 | NP_001377.1 | |||
DPYSL2 | NM_001244604.2 | c.*949G>A | 3_prime_UTR_variant | Exon 14 of 14 | NP_001231533.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DPYSL2 | ENST00000521913.7 | c.*949G>A | 3_prime_UTR_variant | Exon 14 of 14 | 1 | NM_001197293.3 | ENSP00000427985.2 | |||
DPYSL2 | ENST00000311151.9 | c.*949G>A | 3_prime_UTR_variant | Exon 14 of 14 | 1 | ENSP00000309539.5 |
Frequencies
GnomAD3 genomes AF: 0.0136 AC: 2064AN: 152104Hom.: 53 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
2064
AN:
152104
Hom.:
Cov.:
31
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:
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 512Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 310
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
512
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
310
African (AFR)
AF:
AC:
0
AN:
4
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AF:
AC:
0
AN:
434
Middle Eastern (MID)
AF:
AC:
0
AN:
2
European-Non Finnish (NFE)
AF:
AC:
0
AN:
62
Other (OTH)
AF:
AC:
0
AN:
10
GnomAD4 genome AF: 0.0136 AC: 2069AN: 152222Hom.: 53 Cov.: 31 AF XY: 0.0134 AC XY: 1001AN XY: 74432 show subpopulations
GnomAD4 genome
AF:
AC:
2069
AN:
152222
Hom.:
Cov.:
31
AF XY:
AC XY:
1001
AN XY:
74432
show subpopulations
African (AFR)
AF:
AC:
1909
AN:
41534
American (AMR)
AF:
AC:
64
AN:
15294
Ashkenazi Jewish (ASJ)
AF:
AC:
35
AN:
3472
East Asian (EAS)
AF:
AC:
2
AN:
5186
South Asian (SAS)
AF:
AC:
2
AN:
4812
European-Finnish (FIN)
AF:
AC:
0
AN:
10602
Middle Eastern (MID)
AF:
AC:
3
AN:
294
European-Non Finnish (NFE)
AF:
AC:
30
AN:
68008
Other (OTH)
AF:
AC:
24
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.511
Heterozygous variant carriers
0
99
199
298
398
497
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
24
48
72
96
120
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
8
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
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
Publications
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