7-34958238-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001366673.1(DPY19L1):​c.1093-168T>C 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 152,130 control chromosomes in the GnomAD database, including 5,717 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 ( 5717 hom., cov: 32)

Consequence

DPY19L1
NM_001366673.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0120
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
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/exons MANE Protein UniProt
DPY19L1NM_001366673.1 linkuse as main transcriptc.1093-168T>C intron_variant ENST00000638088.2 NP_001353602.1
DPY19L1NM_015283.2 linkuse as main transcriptc.874-168T>C intron_variant NP_056098.1
DPY19L1XM_011515246.4 linkuse as main transcriptc.1093-2871T>C intron_variant XP_011513548.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
DPY19L1ENST00000638088.2 linkuse as main transcriptc.1093-168T>C intron_variant 5 NM_001366673.1 ENSP00000490722 P1

Frequencies

GnomAD3 genomes
AF:
0.270
AC:
41003
AN:
152012
Hom.:
5705
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.212
Gnomad AMI
AF:
0.273
Gnomad AMR
AF:
0.254
Gnomad ASJ
AF:
0.339
Gnomad EAS
AF:
0.151
Gnomad SAS
AF:
0.225
Gnomad FIN
AF:
0.306
Gnomad MID
AF:
0.250
Gnomad NFE
AF:
0.311
Gnomad OTH
AF:
0.293
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.270
AC:
41045
AN:
152130
Hom.:
5717
Cov.:
32
AF XY:
0.267
AC XY:
19858
AN XY:
74388
show subpopulations
Gnomad4 AFR
AF:
0.212
Gnomad4 AMR
AF:
0.254
Gnomad4 ASJ
AF:
0.339
Gnomad4 EAS
AF:
0.151
Gnomad4 SAS
AF:
0.226
Gnomad4 FIN
AF:
0.306
Gnomad4 NFE
AF:
0.311
Gnomad4 OTH
AF:
0.290
Alfa
AF:
0.297
Hom.:
3176
Bravo
AF:
0.266
Asia WGS
AF:
0.183
AC:
635
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
1.1
DANN
Benign
0.77

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1637673; hg19: chr7-34997850; API