chr2-26930006-C-T

Position:

• chr2-26930006-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020134.4(DPYSL5):​c.670-1634C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 152,040 control chromosomes in the GnomAD database, including 6,672 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 0.29 (6672 hom., cov: 33)
• Consequence: DPYSL5 NM_020134.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.450

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DPYSL5	NM_020134.4	c.670-1634C>T		intron_variant		ENST00000288699.11
DPYSL5	NM_001253723.2	c.670-1634C>T		intron_variant
DPYSL5	NM_001253724.2	c.670-1634C>T		intron_variant
DPYSL5	XM_024453007.2	c.670-1634C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DPYSL5	ENST00000288699.11	c.670-1634C>T		intron_variant		1	NM_020134.4	P1
DPYSL5	ENST00000401478.5	c.670-1634C>T		intron_variant		1		P1
DPYSL5	ENST00000614712.4	c.670-1634C>T		intron_variant		5		P1

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43354 AN: 151922 Hom.: 6652 Cov.: 33

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.266

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.285 AC: 43407 AN: 152040 Hom.: 6672 Cov.: 33 AF XY: 0.282 AC XY: 20935 AN XY: 74320

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.363

Gnomad4 ASJ AF: 0.224

Gnomad4 EAS AF: 0.155

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.271

Alfa AF: 0.259 Hom.: 10777

Bravo AF: 0.305

Asia WGS AF: 0.201 AC: 699 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.66

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

Other links and lift over

dbSNP: rs1371614; hg19: chr2-27152874;