chrX-50901254-C-T

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 0.0513 in 111,563 control chromosomes in the GnomAD database, including 158 homozygotes. There are 1,617 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 0.051 ( 158 hom., 1617 hem., cov: 22)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.152

Publications

1 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=-0.92).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.071 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:
0.0512
AC:
5713
AN:
111509
Hom.:
158
Cov.:
22
show subpopulations
Gnomad AFR
AF:
0.0172
Gnomad AMI
AF:
0.0145
Gnomad AMR
AF:
0.0298
Gnomad ASJ
AF:
0.0930
Gnomad EAS
AF:
0.0101
Gnomad SAS
AF:
0.0758
Gnomad FIN
AF:
0.0686
Gnomad MID
AF:
0.0672
Gnomad NFE
AF:
0.0729
Gnomad OTH
AF:
0.0569
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0513
AC:
5718
AN:
111563
Hom.:
158
Cov.:
22
AF XY:
0.0479
AC XY:
1617
AN XY:
33745
show subpopulations
African (AFR)
AF:
0.0173
AC:
532
AN:
30745
American (AMR)
AF:
0.0298
AC:
313
AN:
10500
Ashkenazi Jewish (ASJ)
AF:
0.0930
AC:
245
AN:
2633
East Asian (EAS)
AF:
0.0102
AC:
36
AN:
3539
South Asian (SAS)
AF:
0.0753
AC:
196
AN:
2603
European-Finnish (FIN)
AF:
0.0686
AC:
413
AN:
6020
Middle Eastern (MID)
AF:
0.0737
AC:
16
AN:
217
European-Non Finnish (NFE)
AF:
0.0729
AC:
3869
AN:
53088
Other (OTH)
AF:
0.0576
AC:
88
AN:
1529
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
190
380
571
761
951
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
64
128
192
256
320
<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:
0.0708
Hom.:
921
Bravo
AF:
0.0465

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
1.7
DANN
Benign
0.28
PhyloP100
0.15

Splicing

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

Publications

Other links and lift over

dbSNP: rs17249566; hg19: chrX-50644254; API