dbSNP rs741441: DPY19L3:c.-37-49G>A (chr19-32408168-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -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

Publications

12 publications found

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:

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=-0.84).

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 rank	MANE	Protein	UniProt
DPY19L3	NM_001172774.2 link	c.-37-49G>A		intron_variant	Intron 1 of 18	ENST00000392250.7	NP_001166245.1	Q6ZPD9-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DPY19L3	ENST00000392250.7 link	c.-37-49G>A		intron_variant	Intron 1 of 18	5	NM_001172774.2	ENSP00000376081.2		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

African (AFR)

AF:

0.163

AC:

2994

AN:

18348

American (AMR)

AF:

0.269

AC:

9123

AN:

33884

Ashkenazi Jewish (ASJ)

AF:

0.494

AC:

9352

AN:

18914

East Asian (EAS)

AF:

0.143

AC:

5156

AN:

36014

South Asian (SAS)

AF:

0.318

AC:

20301

AN:

63920

European-Finnish (FIN)

AF:

0.512

AC:

26427

AN:

51598

Middle Eastern (MID)

AF:

0.426

AC:

1111

AN:

2606

European-Non Finnish (NFE)

AF:

0.531

AC:

248773

AN:

468542

Other (OTH)

AF:

0.446

AC:

15878

AN:

35622

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

8468

16936

25405

33873

42341

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.391

AC:

59421

AN:

152000

Hom.:

13670

Cov.:

AF XY:

0.389

AC XY:

28905

AN XY:

74258

show subpopulations

African (AFR)

AF:

0.169

AC:

7022

AN:

41500

American (AMR)

AF:

0.345

AC:

5266

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.494

AC:

1715

AN:

3472

East Asian (EAS)

AF:

0.180

AC:

926

AN:

5152

South Asian (SAS)

AF:

0.315

AC:

1518

AN:

4812

European-Finnish (FIN)

AF:

0.502

AC:

5289

AN:

10540

Middle Eastern (MID)

AF:

0.411

AC:

120

AN:

292

European-Non Finnish (NFE)

AF:

0.532

AC:

36144

AN:

67940

Other (OTH)

AF:

0.402

AC:

849

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1645

3289

4934

6578

8223

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.487

Hom.:

11186

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

(source)

DANN

Benign

0.71

PhyloP100

0.66

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

rs741441

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