rs16967057

chr19-32423172-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001172774.2(DPY19L3):c.238-9544A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,126 control chromosomes in the GnomAD database, including 2,813 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 0.19 (2813 hom., cov: 31)
• Consequence: DPY19L3 NM_001172774.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.51

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DPY19L3	NM_001172774.2	c.238-9544A>C		intron_variant		ENST00000392250.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DPY19L3	ENST00000392250.7	c.238-9544A>C		intron_variant		5	NM_001172774.2	P1

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28652 AN: 152008 Hom.: 2805 Cov.: 31

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.181

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.189 AC: 28677 AN: 152126 Hom.: 2813 Cov.: 31 AF XY: 0.189 AC XY: 14034 AN XY: 74368

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.228

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.179

Alfa AF: 0.183 Hom.: 467

Bravo AF: 0.189

Asia WGS AF: 0.129 AC: 450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
Cadd	Benign	11
Dann	Benign	0.79

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

LitVar

Other links and lift over

dbSNP: rs16967057; hg19: chr19-32914078;