X-866815-T-G

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 0.447 in 151,502 control chromosomes in the GnomAD database, including 15,803 homozygotes. There are 32,536 hemizygotes in GnomAD. 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 0.45 ( 15803 hom., 32536 hem., cov: 29)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.09

Publications

0 publications found
Variant links:

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ACMG classification

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

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.447
AC:
67598
AN:
151386
Hom.:
15762
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.568
Gnomad AMI
AF:
0.333
Gnomad AMR
AF:
0.426
Gnomad ASJ
AF:
0.307
Gnomad EAS
AF:
0.455
Gnomad SAS
AF:
0.377
Gnomad FIN
AF:
0.308
Gnomad MID
AF:
0.349
Gnomad NFE
AF:
0.412
Gnomad OTH
AF:
0.441
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.447
AC:
67694
AN:
151502
Hom.:
15803
Cov.:
29
AF XY:
0.440
AC XY:
32536
AN XY:
73970
show subpopulations
African (AFR)
AF:
0.569
AC:
23513
AN:
41310
American (AMR)
AF:
0.425
AC:
6459
AN:
15182
Ashkenazi Jewish (ASJ)
AF:
0.307
AC:
1064
AN:
3462
East Asian (EAS)
AF:
0.455
AC:
2328
AN:
5114
South Asian (SAS)
AF:
0.377
AC:
1808
AN:
4802
European-Finnish (FIN)
AF:
0.308
AC:
3229
AN:
10494
Middle Eastern (MID)
AF:
0.344
AC:
99
AN:
288
European-Non Finnish (NFE)
AF:
0.412
AC:
27969
AN:
67848
Other (OTH)
AF:
0.441
AC:
922
AN:
2092
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.507
Heterozygous variant carriers
0
1811
3621
5432
7242
9053
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
622
1244
1866
2488
3110
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Bravo
AF:
0.463

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.57
CADD
Benign
0.041
DANN
Benign
0.30
PhyloP100
-1.1

Splicing

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

Publications

Other links and lift over

dbSNP: rs5946520; hg19: chrX-827550; API