GeneBe

chr14-21767650-A-G

Variant names:

Variant summary

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

The variant allele was found at a frequency of 0.347 in 151,862 control chromosomes in the GnomAD database, including 9,389 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 0.35 ( 9389 hom., cov: 30)

Consequence

TRA
intragenic

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.668

Publications

7 publications found
Variant links:
Genes affected

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 (Cadd=9.915).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TRA n.21767650A>G intragenic_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.347
AC:
52673
AN:
151742
Hom.:
9384
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.313
Gnomad AMI
AF:
0.311
Gnomad AMR
AF:
0.287
Gnomad ASJ
AF:
0.393
Gnomad EAS
AF:
0.217
Gnomad SAS
AF:
0.279
Gnomad FIN
AF:
0.358
Gnomad MID
AF:
0.285
Gnomad NFE
AF:
0.393
Gnomad OTH
AF:
0.338
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.347
AC:
52690
AN:
151862
Hom.:
9389
Cov.:
30
AF XY:
0.343
AC XY:
25425
AN XY:
74214
show subpopulations
African (AFR)
AF:
0.313
AC:
12964
AN:
41432
American (AMR)
AF:
0.287
AC:
4376
AN:
15244
Ashkenazi Jewish (ASJ)
AF:
0.393
AC:
1362
AN:
3470
East Asian (EAS)
AF:
0.217
AC:
1120
AN:
5158
South Asian (SAS)
AF:
0.279
AC:
1342
AN:
4812
European-Finnish (FIN)
AF:
0.358
AC:
3774
AN:
10540
Middle Eastern (MID)
AF:
0.299
AC:
88
AN:
294
European-Non Finnish (NFE)
AF:
0.393
AC:
26667
AN:
67892
Other (OTH)
AF:
0.338
AC:
714
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1721
3442
5164
6885
8606
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
524
1048
1572
2096
2620
<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:
0.361
Hom.:
8809
Bravo
AF:
0.339

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
CADD
Benign
9.9
PhyloP100
0.67

Splicing

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

Publications

Other links and lift over

dbSNP: rs718433; hg19: -; API