Variant rs741441 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001172774.2(DPY19L3):c.-37-49G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 881,448 control chromosomes in the GnomAD database, including 98,648 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 0.39 ( 13670 hom., cov: 31)

Exomes 𝑓: 0.46 ( 84978 hom. )

Consequence

DPY19L3
NM_001172774.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.662

Variant links:

Genes affected

DPY19L3 (HGNC:27120): (dpy-19 like C-mannosyltransferase 3) Predicted to enable mannosyltransferase activity. Predicted to be involved in protein C-linked glycosylation via 2'-alpha-mannosyl-L-tryptophan. Predicted to be integral component of membrane. Predicted to be active in nuclear inner membrane. [provided by Alliance of Genome Resources, Apr 2022]

DPY19L3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DPY19L3	NM_001172774.2 linkuse as main transcript	c.-37-49G>A		intron_variant		ENST00000392250.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DPY19L3	ENST00000392250.7 linkuse as main transcript	c.-37-49G>A		intron_variant		5	NM_001172774.2	P1	Q6ZPD9-1

Frequencies

GnomAD3 genomes

AF:

0.391

AC:

59432

AN:

151882

Hom.:

13673

Cov.:

show subpopulations

Gnomad AFR

AF:

0.170

Gnomad AMI

AF:

0.630

Gnomad AMR

AF:

0.345

Gnomad ASJ

AF:

0.494

Gnomad EAS

AF:

0.180

Gnomad SAS

AF:

0.316

Gnomad FIN

AF:

0.502

Gnomad MID

AF:

0.430

Gnomad NFE

AF:

0.532

Gnomad OTH

AF:

0.403

GnomAD4 exome

AF:

0.465

AC:

339115

AN:

729448

Hom.:

84978

Cov.:

AF XY:

0.463

AC XY:

178404

AN XY:

385696

show subpopulations

Gnomad4 AFR exome

AF:

0.163

Gnomad4 AMR exome

AF:

0.269

Gnomad4 ASJ exome

AF:

0.494

Gnomad4 EAS exome

AF:

0.143

Gnomad4 SAS exome

AF:

0.318

Gnomad4 FIN exome

AF:

0.512

Gnomad4 NFE exome

AF:

0.531

Gnomad4 OTH exome

AF:

0.446

GnomAD4 genome

AF:

0.391

AC:

59421

AN:

152000

Hom.:

13670

Cov.:

AF XY:

0.389

AC XY:

28905

AN XY:

74258

show subpopulations

Gnomad4 AFR

AF:

0.169

Gnomad4 AMR

AF:

0.345

Gnomad4 ASJ

AF:

0.494

Gnomad4 EAS

AF:

0.180

Gnomad4 SAS

AF:

0.315

Gnomad4 FIN

AF:

0.502

Gnomad4 NFE

AF:

0.532

Gnomad4 OTH

AF:

0.402

Alfa

AF:

0.488

Hom.:

10177

Bravo

AF:

0.369

Asia WGS

AF:

0.235

AC:

820

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

4.5

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over