GeneBe

ENST00000440005.6:n.135-8411G>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.135-8411G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0983 in 151,850 control chromosomes in the GnomAD database, including 888 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 0.098 ( 888 hom., cov: 30)

Consequence

DGCR5
ENST00000440005.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.208

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=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DGCR5NR_002733.3 linkn.192-8411G>A intron_variant Intron 1 of 3
DGCR5NR_024159.2 linkn.191+8688G>A intron_variant Intron 1 of 4
DGCR5NR_026651.2 linkn.191+8688G>A intron_variant Intron 1 of 4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DGCR5ENST00000440005.6 linkn.135-8411G>A intron_variant Intron 1 of 5 1
DGCR5ENST00000421572.2 linkn.145-6490G>A intron_variant Intron 1 of 5 2
DGCR5ENST00000438934.5 linkn.146-8411G>A intron_variant Intron 1 of 4 5

Frequencies

GnomAD3 genomes
AF:
0.0983
AC:
14912
AN:
151732
Hom.:
884
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.163
Gnomad AMI
AF:
0.0844
Gnomad AMR
AF:
0.0669
Gnomad ASJ
AF:
0.0637
Gnomad EAS
AF:
0.000580
Gnomad SAS
AF:
0.0154
Gnomad FIN
AF:
0.0416
Gnomad MID
AF:
0.0696
Gnomad NFE
AF:
0.0905
Gnomad OTH
AF:
0.0961
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0983
AC:
14928
AN:
151850
Hom.:
888
Cov.:
30
AF XY:
0.0941
AC XY:
6988
AN XY:
74222
show subpopulations
African (AFR)
AF:
0.163
AC:
6725
AN:
41364
American (AMR)
AF:
0.0668
AC:
1018
AN:
15246
Ashkenazi Jewish (ASJ)
AF:
0.0637
AC:
221
AN:
3468
East Asian (EAS)
AF:
0.000581
AC:
3
AN:
5160
South Asian (SAS)
AF:
0.0154
AC:
74
AN:
4790
European-Finnish (FIN)
AF:
0.0416
AC:
440
AN:
10568
Middle Eastern (MID)
AF:
0.0646
AC:
19
AN:
294
European-Non Finnish (NFE)
AF:
0.0905
AC:
6152
AN:
67944
Other (OTH)
AF:
0.0946
AC:
199
AN:
2104
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.495
Heterozygous variant carriers
0
630
1260
1890
2520
3150
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
158
316
474
632
790
<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:
0.0893
Hom.:
701
Bravo
AF:
0.104
Asia WGS
AF:
0.0190
AC:
67
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
3.1
DANN
Benign
0.59
PhyloP100
0.21

Splicing

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

Publications

Other links and lift over

dbSNP: rs2078743; hg19: chr22-18966859; API