rs3829809

Variant summary

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

The ENST00000518707.1(DMGDH):​n.128+8102G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 152,180 control chromosomes in the GnomAD database, including 8,032 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 0.30 ( 8032 hom., cov: 32)

Consequence

DMGDH
ENST00000518707.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.458
Variant links:
Genes affected

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=-0.9).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LOC124901011XR_007058835.1 linkuse as main transcriptn.214-3783G>C intron_variant
LOC124901011XR_007058836.1 linkuse as main transcriptn.213+8102G>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
DMGDHENST00000518707.1 linkuse as main transcriptn.128+8102G>C intron_variant 2
DMGDHENST00000520388.5 linkuse as main transcriptn.228+8102G>C intron_variant 4
DMGDHENST00000520855.1 linkuse as main transcriptn.196-3783G>C intron_variant 3

Frequencies

GnomAD3 genomes
AF:
0.296
AC:
45044
AN:
152062
Hom.:
8028
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0857
Gnomad AMI
AF:
0.541
Gnomad AMR
AF:
0.401
Gnomad ASJ
AF:
0.335
Gnomad EAS
AF:
0.431
Gnomad SAS
AF:
0.447
Gnomad FIN
AF:
0.436
Gnomad MID
AF:
0.389
Gnomad NFE
AF:
0.352
Gnomad OTH
AF:
0.319
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.296
AC:
45053
AN:
152180
Hom.:
8032
Cov.:
32
AF XY:
0.305
AC XY:
22687
AN XY:
74366
show subpopulations
Gnomad4 AFR
AF:
0.0855
Gnomad4 AMR
AF:
0.402
Gnomad4 ASJ
AF:
0.335
Gnomad4 EAS
AF:
0.431
Gnomad4 SAS
AF:
0.448
Gnomad4 FIN
AF:
0.436
Gnomad4 NFE
AF:
0.352
Gnomad4 OTH
AF:
0.318
Alfa
AF:
0.314
Hom.:
1011
Bravo
AF:
0.284
Asia WGS
AF:
0.421
AC:
1461
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.41
DANN
Benign
0.68

Splicing

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: rs3829809; hg19: chr5-78523532; COSMIC: COSV72897594; API