rs2023328

Variant summary

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

The NM_001366673.1(DPY19L1):​c.765-2077C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,016 control chromosomes in the GnomAD database, including 3,306 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 ( 3306 hom., cov: 32)

Consequence

DPY19L1
NM_001366673.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.480
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
DPY19L1NM_001366673.1 linkuse as main transcriptc.765-2077C>T intron_variant ENST00000638088.2
DPY19L1NM_015283.2 linkuse as main transcriptc.546-2077C>T intron_variant
DPY19L1XM_011515246.4 linkuse as main transcriptc.765-2077C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
DPY19L1ENST00000638088.2 linkuse as main transcriptc.765-2077C>T intron_variant 5 NM_001366673.1 P1

Frequencies

GnomAD3 genomes
AF:
0.196
AC:
29812
AN:
151896
Hom.:
3301
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.169
Gnomad AMI
AF:
0.144
Gnomad AMR
AF:
0.352
Gnomad ASJ
AF:
0.115
Gnomad EAS
AF:
0.212
Gnomad SAS
AF:
0.151
Gnomad FIN
AF:
0.236
Gnomad MID
AF:
0.131
Gnomad NFE
AF:
0.179
Gnomad OTH
AF:
0.184
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.196
AC:
29834
AN:
152016
Hom.:
3306
Cov.:
32
AF XY:
0.204
AC XY:
15121
AN XY:
74302
show subpopulations
Gnomad4 AFR
AF:
0.169
Gnomad4 AMR
AF:
0.353
Gnomad4 ASJ
AF:
0.115
Gnomad4 EAS
AF:
0.213
Gnomad4 SAS
AF:
0.151
Gnomad4 FIN
AF:
0.236
Gnomad4 NFE
AF:
0.179
Gnomad4 OTH
AF:
0.184
Alfa
AF:
0.186
Hom.:
3901
Bravo
AF:
0.204
Asia WGS
AF:
0.181
AC:
630
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
1.9
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: rs2023328; hg19: chr7-35031630; API