rs1186717

chr7-34931297-G-T

Variant summary

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

The NM_001366673.1(DPY19L1):c.*276C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 241,172 control chromosomes in the GnomAD database, including 10,311 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 (5849 hom., cov: 32)
  • Exomes 𝑓: 0.31 (4462 hom.)
• Consequence: DPY19L1 NM_001366673.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0210

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=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DPY19L1	NM_001366673.1	c.*276C>A		3_prime_UTR_variant	22/22	ENST00000638088.2
DPY19L1	NM_015283.2	c.*276C>A		3_prime_UTR_variant	22/22
DPY19L1	XM_011515246.4	c.*276C>A		3_prime_UTR_variant	21/21

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DPY19L1	ENST00000638088.2	c.*276C>A		3_prime_UTR_variant	22/22	5	NM_001366673.1	P1

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41146 AN: 151888 Hom.: 5840 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.295

GnomAD4 exome AF: 0.307 AC: 27350 AN: 89166 Hom.: 4462 Cov.: 3 AF XY: 0.306 AC XY: 13871 AN XY: 45336

Gnomad4 AFR exome AF: 0.205

Gnomad4 AMR exome AF: 0.245

Gnomad4 ASJ exome AF: 0.363

Gnomad4 EAS exome AF: 0.132

Gnomad4 SAS exome AF: 0.204

Gnomad4 FIN exome AF: 0.315

Gnomad4 NFE exome AF: 0.330

Gnomad4 OTH exome AF: 0.311

GnomAD4 genome AF: 0.271 AC: 41177 AN: 152006 Hom.: 5849 Cov.: 32 AF XY: 0.268 AC XY: 19906 AN XY: 74290

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.293

Alfa AF: 0.307 Hom.: 3703

Bravo AF: 0.264

Asia WGS AF: 0.171 AC: 597 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	7.9
Dann	Benign	0.82

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: rs1186717; hg19: chr7-34970909;