dbSNP rs11863: DPYSL2:c.*1094C>T (chr8-26656800-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001197293.3(DPYSL2):c.*1094C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 152,612 control chromosomes in the GnomAD database, including 13,805 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 0.41 ( 13724 hom., cov: 32)

Exomes 𝑓: 0.54 ( 81 hom. )

Consequence

DPYSL2
NM_001197293.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.30

Publications

10 publications found

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]

DPYSL2 Gene-Disease associations (from GenCC):

schizophrenia
Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

DPYSL2 links:

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=-0.88).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
DPYSL2	NM_001197293.3 link	c.*1094C>T	3_prime_UTR_variant	Exon 14 of 14	ENST00000521913.7	NP_001184222.1	Q16555Q59GB4A0A1C7CYX9
DPYSL2	NM_001386.6 link	c.*1094C>T	3_prime_UTR_variant	Exon 14 of 14		NP_001377.1	Q16555-1
DPYSL2	NM_001244604.2 link	c.*1094C>T	3_prime_UTR_variant	Exon 14 of 14		NP_001231533.1	Q16555-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DPYSL2	ENST00000521913.7 link	c.*1094C>T		3_prime_UTR_variant	Exon 14 of 14	1	NM_001197293.3	ENSP00000427985.2		A0A1C7CYX9
DPYSL2	ENST00000311151.9 link	c.*1094C>T		3_prime_UTR_variant	Exon 14 of 14	1		ENSP00000309539.5		Q16555-1

Frequencies

GnomAD3 genomes

AF:

0.412

AC:

62564

AN:

151964

Hom.:

13731

Cov.:

show subpopulations

Gnomad AFR

AF:

0.301

Gnomad AMI

AF:

0.504

Gnomad AMR

AF:

0.308

Gnomad ASJ

AF:

0.451

Gnomad EAS

AF:

0.356

Gnomad SAS

AF:

0.319

Gnomad FIN

AF:

0.539

Gnomad MID

AF:

0.348

Gnomad NFE

AF:

0.491

Gnomad OTH

AF:

0.394

GnomAD4 exome

AF:

0.543

AC:

288

AN:

530

Hom.:

Cov.:

AF XY:

0.518

AC XY:

173

AN XY:

334

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.560

AC:

242

AN:

432

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.412

AC:

AN:

Other (OTH)

AF:

0.625

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.493

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.411

AC:

62566

AN:

152082

Hom.:

13724

Cov.:

AF XY:

0.408

AC XY:

30290

AN XY:

74308

show subpopulations

African (AFR)

AF:

0.301

AC:

12484

AN:

41500

American (AMR)

AF:

0.307

AC:

4693

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.451

AC:

1563

AN:

3468

East Asian (EAS)

AF:

0.356

AC:

1833

AN:

5154

South Asian (SAS)

AF:

0.317

AC:

1525

AN:

4812

European-Finnish (FIN)

AF:

0.539

AC:

5697

AN:

10576

Middle Eastern (MID)

AF:

0.330

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.491

AC:

33387

AN:

67972

Other (OTH)

AF:

0.392

AC:

827

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1837

3674

5510

7347

9184

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.472

Hom.:

15664

Bravo

AF:

0.391

Asia WGS

AF:

0.319

AC:

1110

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.012

(source)

DANN

Benign

0.54

PhyloP100

-2.3

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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rs11863

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over