chr5-1168929-G-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 0.115 in 152,076 control chromosomes in the GnomAD database, including 1,216 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 0.11 ( 1216 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.365

Publications

6 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=-0.89).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.215 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:
0.114
AC:
17391
AN:
151958
Hom.:
1210
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.118
Gnomad AMI
AF:
0.107
Gnomad AMR
AF:
0.222
Gnomad ASJ
AF:
0.198
Gnomad EAS
AF:
0.0993
Gnomad SAS
AF:
0.119
Gnomad FIN
AF:
0.0545
Gnomad MID
AF:
0.259
Gnomad NFE
AF:
0.0926
Gnomad OTH
AF:
0.141
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.115
AC:
17421
AN:
152076
Hom.:
1216
Cov.:
32
AF XY:
0.116
AC XY:
8633
AN XY:
74336
show subpopulations
African (AFR)
AF:
0.119
AC:
4921
AN:
41468
American (AMR)
AF:
0.221
AC:
3382
AN:
15274
Ashkenazi Jewish (ASJ)
AF:
0.198
AC:
689
AN:
3472
East Asian (EAS)
AF:
0.0990
AC:
511
AN:
5162
South Asian (SAS)
AF:
0.119
AC:
575
AN:
4822
European-Finnish (FIN)
AF:
0.0545
AC:
576
AN:
10566
Middle Eastern (MID)
AF:
0.259
AC:
76
AN:
294
European-Non Finnish (NFE)
AF:
0.0926
AC:
6297
AN:
67992
Other (OTH)
AF:
0.140
AC:
296
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.498
Heterozygous variant carriers
0
748
1497
2245
2994
3742
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
200
400
600
800
1000
<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:
0.114
Hom.:
1891
Bravo
AF:
0.129
Asia WGS
AF:
0.122
AC:
427
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
1.7
DANN
Benign
0.66
PhyloP100
0.36

Splicing

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

Publications

Other links and lift over

dbSNP: rs7719062; hg19: chr5-1169044; API