GeneBe

chr2-217406996-T-C

Variant names:

Variant summary

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

The ENST00000474063.5(DIRC3):​n.1458+18306A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 151,314 control chromosomes in the GnomAD database, including 18,626 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 0.48 ( 18626 hom., cov: 29)

Consequence

DIRC3
ENST00000474063.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.141

Publications

26 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 -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DIRC3NR_026597.2 linkn.2290+18306A>G intron_variant Intron 8 of 12
DIRC3NR_186292.1 linkn.3529+18306A>G intron_variant Intron 10 of 14
DIRC3NR_186293.1 linkn.2734+18306A>G intron_variant Intron 12 of 16

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DIRC3ENST00000474063.5 linkn.1458+18306A>G intron_variant Intron 7 of 11 2
DIRC3ENST00000486365.6 linkn.2290+18306A>G intron_variant Intron 8 of 12 5
DIRC3ENST00000663562.1 linkn.2377+18306A>G intron_variant Intron 7 of 11

Frequencies

GnomAD3 genomes
AF:
0.481
AC:
72664
AN:
151196
Hom.:
18626
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.369
Gnomad AMI
AF:
0.467
Gnomad AMR
AF:
0.432
Gnomad ASJ
AF:
0.602
Gnomad EAS
AF:
0.232
Gnomad SAS
AF:
0.201
Gnomad FIN
AF:
0.497
Gnomad MID
AF:
0.544
Gnomad NFE
AF:
0.588
Gnomad OTH
AF:
0.514
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.480
AC:
72693
AN:
151314
Hom.:
18626
Cov.:
29
AF XY:
0.472
AC XY:
34855
AN XY:
73852
show subpopulations
African (AFR)
AF:
0.368
AC:
15192
AN:
41230
American (AMR)
AF:
0.431
AC:
6560
AN:
15208
Ashkenazi Jewish (ASJ)
AF:
0.602
AC:
2090
AN:
3470
East Asian (EAS)
AF:
0.232
AC:
1183
AN:
5102
South Asian (SAS)
AF:
0.202
AC:
967
AN:
4788
European-Finnish (FIN)
AF:
0.497
AC:
5147
AN:
10352
Middle Eastern (MID)
AF:
0.544
AC:
160
AN:
294
European-Non Finnish (NFE)
AF:
0.588
AC:
39900
AN:
67852
Other (OTH)
AF:
0.507
AC:
1069
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1779
3558
5337
7116
8895
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
634
1268
1902
2536
3170
<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:
0.549
Hom.:
90053
Bravo
AF:
0.471
Asia WGS
AF:
0.198
AC:
690
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
3.2
DANN
Benign
0.63
PhyloP100
0.14

Splicing

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

Publications

Other links and lift over

dbSNP: rs6759952; hg19: chr2-218271719; API