dbSNP rs763091779: DPY19L1:p.Val488Phe (chr7-34947662-C-A) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001366673.1(DPY19L1):c.1462G>T(p.Val488Phe) variant causes a missense change. The variant allele was found at a frequency of 0.00000479 in 1,460,030 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0000048 ( 0 hom. )

Consequence

DPY19L1
NM_001366673.1 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.71

Variant links:

Genes affected

DPY19L1 (HGNC:22205): (dpy-19 like C-mannosyltransferase 1) Predicted to enable mannosyltransferase activity. Predicted to be involved in protein C-linked glycosylation via 2'-alpha-mannosyl-L-tryptophan. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

DPY19L1 links:

LOC102724723 (HGNC:):

LOC102724723 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DPY19L1	NM_001366673.1 link	c.1462G>T	p.Val488Phe	missense_variant	Exon 15 of 22	ENST00000638088.2	NP_001353602.1
DPY19L1	NM_015283.2 link	c.1243G>T	p.Val415Phe	missense_variant	Exon 15 of 22		NP_056098.1	Q2PZI1-1
DPY19L1	XM_011515246.4 link	c.1375G>T	p.Val459Phe	missense_variant	Exon 14 of 21		XP_011513548.1
LOC102724723	XR_001745166.2 link	n.173-767C>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DPY19L1	ENST00000638088.2 link	c.1462G>T	p.Val488Phe	missense_variant	Exon 15 of 22	5	NM_001366673.1	ENSP00000490722.1		A0A1B0GW05

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000479

AC:

AN:

1460030

Hom.:

Cov.:

AF XY:

0.00000688

AC XY:

AN XY:

726316

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000630

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.45

BayesDel_addAF

Uncertain

0.076

BayesDel_noAF

Benign

-0.13

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.11

.;T;T

Eigen

Uncertain

0.47

Eigen_PC

Uncertain

0.46

FATHMM_MKL

Uncertain

0.93

LIST_S2

Uncertain

0.94

D;D;D

M_CAP

Benign

0.016

MetaRNN

Uncertain

0.48

T;T;T

MetaSVM

Benign

-0.74

MutationAssessor

Uncertain

2.3

.;M;.

PrimateAI

Uncertain

0.62

PROVEAN

Uncertain

-3.3

.;D;D

REVEL

Benign

0.22

Sift

Uncertain

0.018

.;D;D

Sift4G

Uncertain

0.046

.;D;.

Polyphen

0.99

.;D;.

Vest4

0.75

MutPred

0.51

.;Loss of sheet (P = 0.0228);.;

MVP

0.58

MPC

1.1

ClinPred

0.98

GERP RS

5.3

Varity_R

0.38

gMVP

0.69

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.080

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over