Genetic Variant 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001172774.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DPY19L3	NM_001172774.2	MANE Select	c.103+31G>A		intron	N/A	NP_001166245.1
	DPY19L3	NM_207325.3		c.103+31G>A		intron	N/A	NP_997208.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
DPY19L3	ENST00000392250.7	TSL:5 MANE Select	c.103+31G>A	intron	N/A	ENSP00000376081.2
DPY19L3	ENST00000586427.1	TSL:1	c.103+31G>A	intron	N/A	ENSP00000466062.1
DPY19L3	ENST00000587077.6	TSL:1	c.103+31G>A	intron	N/A	ENSP00000465995.1

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 v4.9

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

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

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over