Variant 2-26898526-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_020134.4(DPYSL5):c.27G>A(p.Arg9=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00935 in 1,614,118 control chromosomes in the GnomAD database, including 98 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0062 ( 6 hom., cov: 32)

Exomes 𝑓: 0.0097 ( 92 hom. )

Consequence

DPYSL5
NM_020134.4 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.751

Variant links:

Genes affected

DPYSL5 (HGNC:20637): (dihydropyrimidinase like 5) This gene encodes a member of the CRMP (collapsing response mediator protein) family thought to be involved in neural development. Antibodies to the encoded protein were found in some patients with neurologic symptoms who had paraneoplastic syndrome. A pseudogene of this gene is found on chromosome 11. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Dec 2011]

DPYSL5 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.38).

BP6

Variant 2-26898526-G-A is Benign according to our data. Variant chr2-26898526-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2650752.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.751 with no splicing effect.

BS2

High AC in GnomAd4 at 945 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
DPYSL5	NM_020134.4 linkuse as main transcript	c.27G>A	p.Arg9=	synonymous_variant	2/13	ENST00000288699.11	NP_064519.2
DPYSL5	NM_001253723.2 linkuse as main transcript	c.27G>A	p.Arg9=	synonymous_variant	2/13		NP_001240652.1
DPYSL5	NM_001253724.2 linkuse as main transcript	c.27G>A	p.Arg9=	synonymous_variant	2/13		NP_001240653.1
DPYSL5	XM_024453007.2 linkuse as main transcript	c.27G>A	p.Arg9=	synonymous_variant	2/13		XP_024308775.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DPYSL5	ENST00000288699.11 linkuse as main transcript	c.27G>A	p.Arg9=	synonymous_variant	2/13	1	NM_020134.4	ENSP00000288699	P1

Frequencies

GnomAD3 genomes

AF:

0.00620

AC:

944

AN:

152144

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00154

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00255

Gnomad ASJ

AF:

0.000576

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00145

Gnomad FIN

AF:

0.0182

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00929

Gnomad OTH

AF:

0.00239

GnomAD3 exomes

AF:

0.00685

AC:

1721

AN:

251234

Hom.:

AF XY:

0.00700

AC XY:

950

AN XY:

135792

show subpopulations

Gnomad AFR exome

AF:

0.00166

Gnomad AMR exome

AF:

0.00165

Gnomad ASJ exome

AF:

0.000497

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00189

Gnomad FIN exome

AF:

0.0162

Gnomad NFE exome

AF:

0.0104

Gnomad OTH exome

AF:

0.00734

GnomAD4 exome

AF:

0.00968

AC:

14151

AN:

1461856

Hom.:

Cov.:

AF XY:

0.00948

AC XY:

6897

AN XY:

727220

show subpopulations

Gnomad4 AFR exome

AF:

0.00161

Gnomad4 AMR exome

AF:

0.00152

Gnomad4 ASJ exome

AF:

0.000421

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00201

Gnomad4 FIN exome

AF:

0.0160

Gnomad4 NFE exome

AF:

0.0112

Gnomad4 OTH exome

AF:

0.00803

GnomAD4 genome

AF:

0.00621

AC:

945

AN:

152262

Hom.:

Cov.:

AF XY:

0.00663

AC XY:

494

AN XY:

74454

show subpopulations

Gnomad4 AFR

AF:

0.00154

Gnomad4 AMR

AF:

0.00255

Gnomad4 ASJ

AF:

0.000576

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00145

Gnomad4 FIN

AF:

0.0182

Gnomad4 NFE

AF:

0.00931

Gnomad4 OTH

AF:

0.00237

Alfa

AF:

0.00729

Hom.:

Bravo

AF:

0.00510

Asia WGS

AF:

0.000289

AC:

AN:

3478

EpiCase

AF:

0.00905

EpiControl

AF:

0.00853

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jun 01, 2024

DPYSL5: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.38

CADD

Benign

8.0

DANN

Benign

0.71

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over