chr7-34970582-T-G

Variant names:

• chr7-34970582-T-G
• rs4236340
• NM_001366673.1:c.915-1050A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001366673.1(DPY19L1):​c.915-1050A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 152,078 control chromosomes in the GnomAD database, including 3,319 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 (3319 hom., cov: 32)
• Consequence: DPY19L1 NM_001366673.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.848
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DPY19L1	NM_001366673.1	c.915-1050A>C		intron_variant	Intron 8 of 21	ENST00000638088.2	NP_001353602.1
DPY19L1	NM_015283.2	c.696-1050A>C		intron_variant	Intron 8 of 21		NP_056098.1
DPY19L1	XM_011515246.4	c.915-1050A>C		intron_variant	Intron 8 of 20		XP_011513548.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DPY19L1	ENST00000638088.2	c.915-1050A>C		intron_variant	Intron 8 of 21	5	NM_001366673.1	ENSP00000490722.1

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29875 AN: 151960 Hom.: 3313 Cov.: 32

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.197 AC: 29898 AN: 152078 Hom.: 3319 Cov.: 32 AF XY: 0.204 AC XY: 15147 AN XY: 74326

African (AFR) AF: 0.169 AC: 7028 AN: 41496

American (AMR) AF: 0.356 AC: 5443 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 397 AN: 3470

East Asian (EAS) AF: 0.213 AC: 1100 AN: 5158

South Asian (SAS) AF: 0.153 AC: 735 AN: 4818

European-Finnish (FIN) AF: 0.235 AC: 2485 AN: 10554

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.179 AC: 12161 AN: 67998

Other (OTH) AF: 0.183 AC: 386 AN: 2110

Alfa AF: 0.153 Hom.: 1042

Bravo AF: 0.205

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	-0.88
CADD	Benign	0.098
DANN	Benign	0.72
PhyloP100		-0.85
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4236340; hg19: chr7-35010194;