rs328906

Variant names:

• chr7-34984303-C-A
• rs328906
• NM_001366673.1:c.822+5581G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001366673.1(DPY19L1):​c.822+5581G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 151,904 control chromosomes in the GnomAD database, including 5,137 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 0.25 (5137 hom., cov: 32)
• Consequence: DPY19L1 NM_001366673.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105
• Publications: 7 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DPY19L1	NM_001366673.1	c.822+5581G>T		intron_variant	Intron 7 of 21	ENST00000638088.2	NP_001353602.1
DPY19L1	NM_015283.2	c.603+5581G>T		intron_variant	Intron 7 of 21		NP_056098.1
DPY19L1	XM_011515246.4	c.822+5581G>T		intron_variant	Intron 7 of 20		XP_011513548.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DPY19L1	ENST00000638088.2	c.822+5581G>T		intron_variant	Intron 7 of 21	5	NM_001366673.1	ENSP00000490722.1

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37233 AN: 151786 Hom.: 5118 Cov.: 32

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.246 AC: 37295 AN: 151904 Hom.: 5137 Cov.: 32 AF XY: 0.250 AC XY: 18562 AN XY: 74236

African (AFR) AF: 0.314 AC: 13005 AN: 41406

American (AMR) AF: 0.379 AC: 5780 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 426 AN: 3466

East Asian (EAS) AF: 0.212 AC: 1094 AN: 5166

South Asian (SAS) AF: 0.162 AC: 778 AN: 4810

European-Finnish (FIN) AF: 0.226 AC: 2385 AN: 10538

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

European-Non Finnish (NFE) AF: 0.194 AC: 13153 AN: 67950

Other (OTH) AF: 0.228 AC: 481 AN: 2112

Alfa AF: 0.213 Hom.: 6522

Bravo AF: 0.260

Asia WGS AF: 0.200 AC: 698 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.66
PhyloP100		0.10
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: rs328906; hg19: chr7-35023915;