dbSNP rs2012353: DPY19L3:c.103+31G>A (chr19-32408387-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.103+31G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 1,543,030 control chromosomes in the GnomAD database, including 22,499 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 0.17 ( 2242 hom., cov: 32)

Exomes 𝑓: 0.17 ( 20257 hom. )

Consequence

DPY19L3
NM_001172774.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.29

Publications

14 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=-0.82).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DPY19L3	NM_001172774.2 link	c.103+31G>A		intron_variant	Intron 2 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.103+31G>A		intron_variant	Intron 2 of 18	5	NM_001172774.2	ENSP00000376081.2		Q6ZPD9-1

Frequencies

GnomAD3 genomes

AF:

0.171

AC:

25928

AN:

151978

Hom.:

2237

Cov.:

show subpopulations

Gnomad AFR

AF:

0.183

Gnomad AMI

AF:

0.0625

Gnomad AMR

AF:

0.160

Gnomad ASJ

AF:

0.142

Gnomad EAS

AF:

0.116

Gnomad SAS

AF:

0.169

Gnomad FIN

AF:

0.228

Gnomad MID

AF:

0.133

Gnomad NFE

AF:

0.164

Gnomad OTH

AF:

0.167

GnomAD2 exomes

AF:

0.173

AC:

41245

AN:

238424

AF XY:

0.172

show subpopulations

Gnomad AFR exome

AF:

0.188

Gnomad AMR exome

AF:

0.204

Gnomad ASJ exome

AF:

0.137

Gnomad EAS exome

AF:

0.129

Gnomad FIN exome

AF:

0.225

Gnomad NFE exome

AF:

0.162

Gnomad OTH exome

AF:

0.167

GnomAD4 exome

AF:

0.169

AC:

235094

AN:

1390934

Hom.:

20257

Cov.:

AF XY:

0.168

AC XY:

116998

AN XY:

695688

show subpopulations

African (AFR)

AF:

0.188

AC:

5938

AN:

31570

American (AMR)

AF:

0.202

AC:

8546

AN:

42338

Ashkenazi Jewish (ASJ)

AF:

0.141

AC:

3575

AN:

25328

East Asian (EAS)

AF:

0.117

AC:

4590

AN:

39260

South Asian (SAS)

AF:

0.171

AC:

14230

AN:

83224

European-Finnish (FIN)

AF:

0.222

AC:

11798

AN:

53202

Middle Eastern (MID)

AF:

0.162

AC:

906

AN:

5598

European-Non Finnish (NFE)

AF:

0.167

AC:

175816

AN:

1052514

Other (OTH)

AF:

0.167

AC:

9695

AN:

57900

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

9539

19077

28616

38154

47693

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6266

12532

18798

25064

31330

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.171

AC:

25950

AN:

152096

Hom.:

2242

Cov.:

AF XY:

0.171

AC XY:

12742

AN XY:

74376

show subpopulations

African (AFR)

AF:

0.183

AC:

7594

AN:

41480

American (AMR)

AF:

0.160

AC:

2442

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.142

AC:

493

AN:

3470

East Asian (EAS)

AF:

0.116

AC:

599

AN:

5184

South Asian (SAS)

AF:

0.170

AC:

817

AN:

4820

European-Finnish (FIN)

AF:

0.228

AC:

2408

AN:

10560

Middle Eastern (MID)

AF:

0.133

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.164

AC:

11152

AN:

67986

Other (OTH)

AF:

0.165

AC:

349

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1107

2213

3320

4426

5533

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

280

560

840

1120

1400

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.165

Hom.:

2830

Bravo

AF:

0.168

Asia WGS

AF:

0.125

AC:

437

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

9.5

(source)

DANN

Benign

0.55

PhyloP100

2.3

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

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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