chr19-32423172-A-C

Variant names:

• chr19-32423172-A-C
• rs16967057
• NM_001172774.2:c.238-9544A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

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.238-9544A>C		intron	N/A	NP_001166245.1
	DPY19L3	NM_207325.3		c.238-9544A>C		intron	N/A	NP_997208.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DPY19L3	ENST00000392250.7	TSL:5 MANE Select	c.238-9544A>C		intron	N/A	ENSP00000376081.2
	DPY19L3	ENST00000586427.1	TSL:1	c.238-9544A>C		intron	N/A	ENSP00000466062.1
	DPY19L3	ENST00000342179.9	TSL:2	c.238-9544A>C		intron	N/A	ENSP00000344937.4

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

African (AFR) AF: 0.243 AC: 10083 AN: 41484

American (AMR) AF: 0.168 AC: 2564 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 492 AN: 3470

East Asian (EAS) AF: 0.115 AC: 598 AN: 5186

South Asian (SAS) AF: 0.170 AC: 820 AN: 4818

European-Finnish (FIN) AF: 0.228 AC: 2408 AN: 10570

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11237 AN: 67990

Other (OTH) AF: 0.179 AC: 379 AN: 2114

Alfa AF: 0.185 Hom.: 494

Bravo AF: 0.189

Asia WGS AF: 0.129 AC: 450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	11
DANN	Benign	0.79
PhyloP100		1.5
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs16967057; hg19: chr19-32914078;