rs5968255

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 0.127 in 111,247 control chromosomes in the GnomAD database, including 873 homozygotes. There are 4,257 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 0.13 ( 873 hom., 4257 hem., cov: 22)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0780

Publications

3 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=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.513 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:
0.127
AC:
14155
AN:
111188
Hom.:
872
Cov.:
22
show subpopulations
Gnomad AFR
AF:
0.0863
Gnomad AMI
AF:
0.0966
Gnomad AMR
AF:
0.136
Gnomad ASJ
AF:
0.134
Gnomad EAS
AF:
0.533
Gnomad SAS
AF:
0.267
Gnomad FIN
AF:
0.141
Gnomad MID
AF:
0.0675
Gnomad NFE
AF:
0.115
Gnomad OTH
AF:
0.116
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.127
AC:
14160
AN:
111247
Hom.:
873
Cov.:
22
AF XY:
0.127
AC XY:
4257
AN XY:
33485
show subpopulations
African (AFR)
AF:
0.0861
AC:
2647
AN:
30728
American (AMR)
AF:
0.136
AC:
1425
AN:
10456
Ashkenazi Jewish (ASJ)
AF:
0.134
AC:
354
AN:
2635
East Asian (EAS)
AF:
0.534
AC:
1845
AN:
3458
South Asian (SAS)
AF:
0.266
AC:
700
AN:
2630
European-Finnish (FIN)
AF:
0.141
AC:
839
AN:
5931
Middle Eastern (MID)
AF:
0.0737
AC:
16
AN:
217
European-Non Finnish (NFE)
AF:
0.115
AC:
6092
AN:
52987
Other (OTH)
AF:
0.116
AC:
176
AN:
1522
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
419
838
1256
1675
2094
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
178
356
534
712
890
<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:
0.124
Hom.:
12151
Bravo
AF:
0.128

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
1.9
DANN
Benign
0.73
PhyloP100
-0.078

Splicing

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

Publications

Other links and lift over

dbSNP: rs5968255; hg19: chrX-83254692; API