GeneBe

chr4-98875633-T-C

Variant names:

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 0.559 in 151,368 control chromosomes in the GnomAD database, including 26,076 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 0.56 ( 26076 hom., cov: 30)
Exomes 𝑓: 0.28 ( 6 hom. )
Failed GnomAD Quality Control

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.76

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=-1.02).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.828 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:
0.559
AC:
84490
AN:
151248
Hom.:
26012
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.835
Gnomad AMI
AF:
0.380
Gnomad AMR
AF:
0.503
Gnomad ASJ
AF:
0.501
Gnomad EAS
AF:
0.681
Gnomad SAS
AF:
0.397
Gnomad FIN
AF:
0.447
Gnomad MID
AF:
0.415
Gnomad NFE
AF:
0.429
Gnomad OTH
AF:
0.552
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.277
AC:
26
AN:
94
Hom.:
6
Cov.:
0
AF XY:
0.256
AC XY:
20
AN XY:
78
show subpopulations
African (AFR)
AF:
0.500
AC:
1
AN:
2
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AF:
0.500
AC:
1
AN:
2
South Asian (SAS)
AF:
0.00
AC:
0
AN:
2
European-Finnish (FIN)
AC:
0
AN:
0
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
2
European-Non Finnish (NFE)
AF:
0.256
AC:
21
AN:
82
Other (OTH)
AF:
0.750
AC:
3
AN:
4
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.468
Heterozygous variant carriers
0
1
2
4
5
6
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
AF:
0.559
AC:
84622
AN:
151368
Hom.:
26076
Cov.:
30
AF XY:
0.555
AC XY:
41029
AN XY:
73924
show subpopulations
African (AFR)
AF:
0.836
AC:
34485
AN:
41266
American (AMR)
AF:
0.503
AC:
7651
AN:
15224
Ashkenazi Jewish (ASJ)
AF:
0.501
AC:
1732
AN:
3460
East Asian (EAS)
AF:
0.681
AC:
3436
AN:
5046
South Asian (SAS)
AF:
0.397
AC:
1913
AN:
4814
European-Finnish (FIN)
AF:
0.447
AC:
4691
AN:
10496
Middle Eastern (MID)
AF:
0.426
AC:
121
AN:
284
European-Non Finnish (NFE)
AF:
0.429
AC:
29093
AN:
67776
Other (OTH)
AF:
0.552
AC:
1156
AN:
2096
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.507
Heterozygous variant carriers
0
1653
3306
4960
6613
8266
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
684
1368
2052
2736
3420
<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:
0.293
Hom.:
2584
Bravo
AF:
0.581
Asia WGS
AF:
0.525
AC:
1831
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
1.1
DANN
Benign
0.11
PhyloP100
-1.8
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs7665590; hg19: chr4-99796784; API