GeneBe

ENST00000440005.6:n.134+5169G>A

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000440005.6(DGCR5):​n.134+5169G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 152,026 control chromosomes in the GnomAD database, including 21,733 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 0.51 ( 21733 hom., cov: 33)

Consequence

DGCR5
ENST00000440005.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.956

Publications

14 publications found
Variant links:
Genes affected
DGCR5 (HGNC:16757): (DiGeorge syndrome critical region gene 5) Biomarker of Huntington's disease. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DGCR5NR_002733.3 linkn.191+5169G>A intron_variant Intron 1 of 3
DGCR5NR_024159.2 linkn.191+5169G>A intron_variant Intron 1 of 4
DGCR5NR_026651.2 linkn.191+5169G>A intron_variant Intron 1 of 4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DGCR5ENST00000440005.6 linkn.134+5169G>A intron_variant Intron 1 of 5 1
DGCR5ENST00000421572.2 linkn.144+5169G>A intron_variant Intron 1 of 5 2
DGCR5ENST00000438934.5 linkn.145+5169G>A intron_variant Intron 1 of 4 5

Frequencies

GnomAD3 genomes
AF:
0.513
AC:
77978
AN:
151908
Hom.:
21732
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.313
Gnomad AMI
AF:
0.746
Gnomad AMR
AF:
0.505
Gnomad ASJ
AF:
0.618
Gnomad EAS
AF:
0.185
Gnomad SAS
AF:
0.615
Gnomad FIN
AF:
0.544
Gnomad MID
AF:
0.563
Gnomad NFE
AF:
0.642
Gnomad OTH
AF:
0.516
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.513
AC:
78001
AN:
152026
Hom.:
21733
Cov.:
33
AF XY:
0.511
AC XY:
37950
AN XY:
74300
show subpopulations
African (AFR)
AF:
0.313
AC:
12960
AN:
41448
American (AMR)
AF:
0.505
AC:
7708
AN:
15278
Ashkenazi Jewish (ASJ)
AF:
0.618
AC:
2140
AN:
3464
East Asian (EAS)
AF:
0.185
AC:
957
AN:
5162
South Asian (SAS)
AF:
0.615
AC:
2962
AN:
4818
European-Finnish (FIN)
AF:
0.544
AC:
5750
AN:
10578
Middle Eastern (MID)
AF:
0.561
AC:
165
AN:
294
European-Non Finnish (NFE)
AF:
0.642
AC:
43597
AN:
67958
Other (OTH)
AF:
0.512
AC:
1082
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
1774
3548
5323
7097
8871
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
678
1356
2034
2712
3390
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.584
Hom.:
19365
Bravo
AF:
0.496
Asia WGS
AF:
0.418
AC:
1458
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
8.2
DANN
Benign
0.49
PhyloP100
0.96

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs2019061; hg19: chr22-18963340; API