rs2101613

Positions:

• chr10-132189263-G-A
• chr10-132189263-G-C

Variant summary

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

The NM_006426.3(DPYSL4):​c.40-1484G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 152,202 control chromosomes in the GnomAD database, including 14,809 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 (14809 hom., cov: 34)
• Consequence: DPYSL4 NM_006426.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.791

Genes affected

DPYSL4 (HGNC:3016): (dihydropyrimidinase like 4) Enables filamin binding activity. Predicted to be involved in nervous system development. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DPYSL4	NM_006426.3	c.40-1484G>A		intron_variant		ENST00000338492.9	NP_006417.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DPYSL4	ENST00000338492.9	c.40-1484G>A		intron_variant		1	NM_006426.3	ENSP00000339850	P1
DPYSL4	ENST00000493882.1	n.45-1484G>A		intron_variant, non_coding_transcript_variant		3
DPYSL4	ENST00000493927.5	n.126-1484G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61798 AN: 152084 Hom.: 14795 Cov.: 34

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.617

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.406 AC: 61813 AN: 152202 Hom.: 14809 Cov.: 34 AF XY: 0.402 AC XY: 29883 AN XY: 74418

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.539

Gnomad4 ASJ AF: 0.419

Gnomad4 EAS AF: 0.326

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.423

Gnomad4 NFE AF: 0.535

Gnomad4 OTH AF: 0.411

Alfa AF: 0.507 Hom.: 27010

Bravo AF: 0.408

Asia WGS AF: 0.312 AC: 1085 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.088
DANN	Benign	0.73

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: rs2101613; hg19: chr10-134002767; COSMIC: COSV53821330; COSMIC: COSV53821330;