7-34981231-C-T

Variant names:

• chr7-34981231-C-T
• rs328902
• NM_001366673.1:c.823-7626G>A

Variant summary

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

The NM_001366673.1(DPY19L1):​c.823-7626G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 151,946 control chromosomes in the GnomAD database, including 5,741 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 (5741 hom., cov: 32)
• Consequence: DPY19L1 NM_001366673.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.766

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=-1.04).
• 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 rank	MANE	Protein	UniProt
DPY19L1	NM_001366673.1	c.823-7626G>A		intron_variant	Intron 7 of 21	ENST00000638088.2	NP_001353602.1
DPY19L1	NM_015283.2	c.604-7626G>A		intron_variant	Intron 7 of 21		NP_056098.1
DPY19L1	XM_011515246.4	c.823-7626G>A		intron_variant	Intron 7 of 20		XP_011513548.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DPY19L1	ENST00000638088.2	c.823-7626G>A		intron_variant	Intron 7 of 21	5	NM_001366673.1	ENSP00000490722.1

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41212 AN: 151828 Hom.: 5729 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.272 AC: 41254 AN: 151946 Hom.: 5741 Cov.: 32 AF XY: 0.269 AC XY: 19946 AN XY: 74228

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.338

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.223

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.292

Alfa AF: 0.304 Hom.: 14172

Bravo AF: 0.267

Asia WGS AF: 0.177 AC: 615 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.57
DANN	Benign	0.27

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: rs328902; hg19: chr7-35020843;