rs2023328

chr7-34992018-G-A

Variant summary

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

The NM_001366673.1(DPY19L1):c.765-2077C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,016 control chromosomes in the GnomAD database, including 3,306 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 0.20 (3306 hom., cov: 32)
• Consequence: DPY19L1 NM_001366673.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.480

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DPY19L1	NM_001366673.1	c.765-2077C>T		intron_variant		ENST00000638088.2
DPY19L1	NM_015283.2	c.546-2077C>T		intron_variant
DPY19L1	XM_011515246.4	c.765-2077C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DPY19L1	ENST00000638088.2	c.765-2077C>T		intron_variant		5	NM_001366673.1	P1

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29812 AN: 151896 Hom.: 3301 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.196 AC: 29834 AN: 152016 Hom.: 3306 Cov.: 32 AF XY: 0.204 AC XY: 15121 AN XY: 74302

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.353

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.213

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.184

Alfa AF: 0.186 Hom.: 3901

Bravo AF: 0.204

Asia WGS AF: 0.181 AC: 630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	1.9
Dann	Benign	0.77

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: rs2023328; hg19: chr7-35031630;