rs1637670

Positions:

• chr7-34955463-A-G

Variant summary

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

The NM_001366673.1(DPY19L1):​c.1180-96T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 1,478,772 control chromosomes in the GnomAD database, including 72,037 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 0.28 (6184 hom., cov: 31)
  • Exomes 𝑓: 0.31 (65853 hom.)
• Consequence: DPY19L1 NM_001366673.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.393

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 (NFE) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DPY19L1	NM_001366673.1	c.1180-96T>C		intron_variant		ENST00000638088.2
DPY19L1	NM_015283.2	c.961-96T>C		intron_variant
DPY19L1	XM_011515246.4	c.1093-96T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DPY19L1	ENST00000638088.2	c.1180-96T>C		intron_variant		5	NM_001366673.1	P1

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42633 AN: 151912 Hom.: 6172 Cov.: 31

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.306

GnomAD4 exome AF: 0.311 AC: 412303 AN: 1326742 Hom.: 65853 AF XY: 0.309 AC XY: 203643 AN XY: 658570

Gnomad4 AFR exome AF: 0.214

Gnomad4 AMR exome AF: 0.234

Gnomad4 ASJ exome AF: 0.361

Gnomad4 EAS exome AF: 0.147

Gnomad4 SAS exome AF: 0.236

Gnomad4 FIN exome AF: 0.310

Gnomad4 NFE exome AF: 0.327

Gnomad4 OTH exome AF: 0.299

GnomAD4 genome AF: 0.281 AC: 42670 AN: 152030 Hom.: 6184 Cov.: 31 AF XY: 0.278 AC XY: 20646 AN XY: 74304

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.304

Alfa AF: 0.294 Hom.: 1150

Bravo AF: 0.276

Asia WGS AF: 0.183 AC: 638 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.5
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: rs1637670; hg19: chr7-34995075;