chr7-34941031-T-C

Position:

• chr7-34941031-T-C

Variant summary

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

The NM_001366673.1(DPY19L1):​c.1690-704A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 151,844 control chromosomes in the GnomAD database, including 5,773 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 (5773 hom., cov: 31)
• Consequence: DPY19L1 NM_001366673.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

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=-0.91).
• 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	Protein	UniProt
DPY19L1	NM_001366673.1	c.1690-704A>G		intron_variant		ENST00000638088.2	NP_001353602.1
DPY19L1	NM_015283.2	c.1471-704A>G		intron_variant			NP_056098.1
DPY19L1	XM_011515246.4	c.1603-704A>G		intron_variant			XP_011513548.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DPY19L1	ENST00000638088.2	c.1690-704A>G		intron_variant		5	NM_001366673.1	ENSP00000490722	P1

Frequencies

GnomAD3 genomes AF: 0.270 AC: 40947 AN: 151726 Hom.: 5764 Cov.: 31

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.270 AC: 40978 AN: 151844 Hom.: 5773 Cov.: 31 AF XY: 0.267 AC XY: 19781 AN XY: 74190

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.292

Alfa AF: 0.159 Hom.: 321

Bravo AF: 0.264

Asia WGS AF: 0.170 AC: 592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.53
DANN	Benign	0.63

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: rs1649215; hg19: chr7-34980643;