GeneBe

rs16857609

Variant names:

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000474063.5(DIRC3):​n.958+1138G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 152,048 control chromosomes in the GnomAD database, including 6,747 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 0.28 ( 6747 hom., cov: 31)

Consequence

DIRC3
ENST00000474063.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.339

Publications

86 publications found
Variant links:
Genes affected
DIRC3 (HGNC:17805): (disrupted in renal carcinoma 3)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.37).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DIRC3NR_026597.2 linkn.1790+1138G>A intron_variant Intron 5 of 12
DIRC3NR_186292.1 linkn.3029+1138G>A intron_variant Intron 7 of 14
DIRC3NR_186293.1 linkn.2234+1138G>A intron_variant Intron 9 of 16

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DIRC3ENST00000474063.5 linkn.958+1138G>A intron_variant Intron 4 of 11 2
DIRC3ENST00000484635.1 linkn.368+1138G>A intron_variant Intron 2 of 4 5
DIRC3ENST00000486365.6 linkn.1790+1138G>A intron_variant Intron 5 of 12 5

Frequencies

GnomAD3 genomes
AF:
0.283
AC:
43050
AN:
151930
Hom.:
6734
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.238
Gnomad AMI
AF:
0.282
Gnomad AMR
AF:
0.328
Gnomad ASJ
AF:
0.273
Gnomad EAS
AF:
0.596
Gnomad SAS
AF:
0.550
Gnomad FIN
AF:
0.300
Gnomad MID
AF:
0.288
Gnomad NFE
AF:
0.257
Gnomad OTH
AF:
0.269
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.283
AC:
43099
AN:
152048
Hom.:
6747
Cov.:
31
AF XY:
0.290
AC XY:
21543
AN XY:
74312
show subpopulations
African (AFR)
AF:
0.238
AC:
9876
AN:
41472
American (AMR)
AF:
0.328
AC:
5020
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
0.273
AC:
947
AN:
3472
East Asian (EAS)
AF:
0.595
AC:
3055
AN:
5134
South Asian (SAS)
AF:
0.550
AC:
2642
AN:
4804
European-Finnish (FIN)
AF:
0.300
AC:
3179
AN:
10584
Middle Eastern (MID)
AF:
0.289
AC:
85
AN:
294
European-Non Finnish (NFE)
AF:
0.257
AC:
17449
AN:
67980
Other (OTH)
AF:
0.279
AC:
589
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1523
3047
4570
6094
7617
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
466
932
1398
1864
2330
<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:
0.271
Hom.:
10448
Bravo
AF:
0.284
Asia WGS
AF:
0.555
AC:
1932
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.37
CADD
Benign
15
DANN
Benign
0.87
PhyloP100
0.34

Splicing

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

Publications

Other links and lift over

dbSNP: rs16857609; hg19: chr2-218296508; API