rs17055641

Variant summary

Our verdict is Benign. Variant got -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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.38
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High AC in GnomAd4 at 2069 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
DPYSL2NM_001197293.3 linkuse as main transcriptc.*949G>A 3_prime_UTR_variant 14/14 ENST00000521913.7
DPYSL2NM_001244604.2 linkuse as main transcriptc.*949G>A 3_prime_UTR_variant 14/14
DPYSL2NM_001386.6 linkuse as main transcriptc.*949G>A 3_prime_UTR_variant 14/14

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
DPYSL2ENST00000521913.7 linkuse as main transcriptc.*949G>A 3_prime_UTR_variant 14/141 NM_001197293.3
DPYSL2ENST00000311151.9 linkuse as main transcriptc.*949G>A 3_prime_UTR_variant 14/141 P1Q16555-1

Frequencies

GnomAD3 genomes
AF:
0.0136
AC:
2064
AN:
152104
Hom.:
53
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0460
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00419
Gnomad ASJ
AF:
0.0101
Gnomad EAS
AF:
0.000385
Gnomad SAS
AF:
0.000415
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00949
Gnomad NFE
AF:
0.000441
Gnomad OTH
AF:
0.0115
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
512
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
310
Gnomad4 AFR exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0136
AC:
2069
AN:
152222
Hom.:
53
Cov.:
31
AF XY:
0.0134
AC XY:
1001
AN XY:
74432
show subpopulations
Gnomad4 AFR
AF:
0.0460
Gnomad4 AMR
AF:
0.00418
Gnomad4 ASJ
AF:
0.0101
Gnomad4 EAS
AF:
0.000386
Gnomad4 SAS
AF:
0.000416
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000441
Gnomad4 OTH
AF:
0.0114
Alfa
AF:
0.0176
Hom.:
6
Bravo
AF:
0.0156
Asia WGS
AF:
0.00231
AC:
8
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
1.2
DANN
Benign
0.47

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs17055641; hg19: chr8-26514171; API