chrX-146609682-T-C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

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 0.79 ( 24126 hom., 25872 hem., cov: 23)
Failed GnomAD Quality Control

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.09

Publications

2 publications found
Variant links:

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ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.99).

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:
0.789
AC:
87049
AN:
110361
Hom.:
24121
Cov.:
23
show subpopulations
Gnomad AFR
AF:
0.813
Gnomad AMI
AF:
0.659
Gnomad AMR
AF:
0.842
Gnomad ASJ
AF:
0.822
Gnomad EAS
AF:
0.793
Gnomad SAS
AF:
0.739
Gnomad FIN
AF:
0.778
Gnomad MID
AF:
0.730
Gnomad NFE
AF:
0.769
Gnomad OTH
AF:
0.770
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Data not reliable, filtered out with message: InbreedingCoeff
AF:
0.789
AC:
87095
AN:
110414
Hom.:
24126
Cov.:
23
AF XY:
0.792
AC XY:
25872
AN XY:
32674
show subpopulations
African (AFR)
AF:
0.812
AC:
24664
AN:
30361
American (AMR)
AF:
0.842
AC:
8717
AN:
10353
Ashkenazi Jewish (ASJ)
AF:
0.822
AC:
2166
AN:
2636
East Asian (EAS)
AF:
0.793
AC:
2747
AN:
3466
South Asian (SAS)
AF:
0.737
AC:
1902
AN:
2579
European-Finnish (FIN)
AF:
0.778
AC:
4548
AN:
5843
Middle Eastern (MID)
AF:
0.723
AC:
154
AN:
213
European-Non Finnish (NFE)
AF:
0.769
AC:
40594
AN:
52793
Other (OTH)
AF:
0.774
AC:
1162
AN:
1501
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
685
1371
2056
2742
3427
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
738
1476
2214
2952
3690
<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:
0.778
Hom.:
112090
Bravo
AF:
0.794

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
0.23
DANN
Benign
0.42
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: rs11094364; hg19: chrX-145691200; API