NM_001366673.1:c.299-232G>A

Variant names:

• chr7-35018828-C-T
• rs329240
• NM_001366673.1:c.299-232G>A

Variant summary

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

The NM_001366673.1(DPY19L1):​c.299-232G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 151,864 control chromosomes in the GnomAD database, including 5,805 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 0.27 (5805 hom., cov: 32)
• Consequence: DPY19L1 NM_001366673.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.782
• Publications: 5 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001366673.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DPY19L1	NM_001366673.1	MANE Select	c.299-232G>A		intron	N/A	NP_001353602.1
	DPY19L1	NM_015283.2		c.80-232G>A		intron	N/A	NP_056098.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DPY19L1	ENST00000638088.2	TSL:5 MANE Select	c.299-232G>A		intron	N/A	ENSP00000490722.1
	DPY19L1	ENST00000310974.8	TSL:1	c.80-232G>A		intron	N/A	ENSP00000308695.4
	DPY19L1	ENST00000944847.1		c.299-232G>A		intron	N/A	ENSP00000614906.1

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41544 AN: 151746 Hom.: 5792 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.274 AC: 41590 AN: 151864 Hom.: 5805 Cov.: 32 AF XY: 0.271 AC XY: 20113 AN XY: 74190

African (AFR) AF: 0.226 AC: 9377 AN: 41406

American (AMR) AF: 0.258 AC: 3943 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1174 AN: 3468

East Asian (EAS) AF: 0.138 AC: 710 AN: 5150

South Asian (SAS) AF: 0.223 AC: 1071 AN: 4812

European-Finnish (FIN) AF: 0.315 AC: 3311 AN: 10504

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.310 AC: 21071 AN: 67944

Other (OTH) AF: 0.290 AC: 611 AN: 2110

Alfa AF: 0.292 Hom.: 4804

Bravo AF: 0.269

Asia WGS AF: 0.178 AC: 618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.8
DANN	Benign	0.76
PhyloP100		-0.78
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: rs329240; hg19: chr7-35058440;