rs329240

chr7-35018828-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DPY19L1	NM_001366673.1	c.299-232G>A		intron_variant		ENST00000638088.2
DPY19L1	NM_015283.2	c.80-232G>A		intron_variant
DPY19L1	XM_011515246.4	c.299-232G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DPY19L1	ENST00000638088.2	c.299-232G>A		intron_variant		5	NM_001366673.1	P1
DPY19L1	ENST00000310974.8	c.80-232G>A		intron_variant		1
DPY19L1	ENST00000481923.1	n.101-232G>A		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.223

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.290

Alfa AF: 0.296 Hom.: 3436

Bravo AF: 0.269

Asia WGS AF: 0.178 AC: 618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.8
Dann	Benign	0.76

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: rs329240; hg19: chr7-35058440;