7-34947662-C-A

Variant names:

• chr7-34947662-C-A
• NM_001366673.1:c.1462G>T

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.71

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]

LOC102724723 (HGNC:):

ACMG classification

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	c.1462G>T	p.Val488Phe	missense_variant	Exon 15 of 22	ENST00000638088.2	NP_001353602.1
DPY19L1	NM_015283.2	c.1243G>T	p.Val415Phe	missense_variant	Exon 15 of 22		NP_056098.1
DPY19L1	XM_011515246.4	c.1375G>T	p.Val459Phe	missense_variant	Exon 14 of 21		XP_011513548.1
LOC102724723	XR_001745166.2	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	c.1462G>T	p.Val488Phe	missense_variant	Exon 15 of 22	5	NM_001366673.1	ENSP00000490722.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000479 AC: 7 AN: 1460030 Hom.: 0 Cov.: 30 AF XY: 0.00000688 AC XY: 5 AN XY: 726316

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.: 32

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	D
BayesDel_noAF	Benign	-0.13
CADD	Benign	23
DANN	Uncertain	0.99
DEOGEN2	Benign	0.11	.;T;T
Eigen	Uncertain	0.47
Eigen_PC	Uncertain	0.46
FATHMM_MKL	Uncertain	0.93	D
LIST_S2	Uncertain	0.94	D;D;D
M_CAP	Benign	0.016	T
MetaRNN	Uncertain	0.48	T;T;T
MetaSVM	Benign	-0.74	T
MutationAssessor	Uncertain	2.3	.;M;.
PrimateAI	Uncertain	0.62	T
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	D
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.

Other links and lift over

hg19: chr7-34987274;