chr4-110728095-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 0.156 in 152,114 control chromosomes in the GnomAD database, including 2,167 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 0.16 ( 2167 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0790

Publications

9 publications found
Variant links:

Genome browser will be placed here

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.343 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:
0.156
AC:
23692
AN:
151996
Hom.:
2164
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.140
Gnomad AMI
AF:
0.0505
Gnomad AMR
AF:
0.208
Gnomad ASJ
AF:
0.324
Gnomad EAS
AF:
0.355
Gnomad SAS
AF:
0.133
Gnomad FIN
AF:
0.150
Gnomad MID
AF:
0.223
Gnomad NFE
AF:
0.133
Gnomad OTH
AF:
0.172
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.156
AC:
23718
AN:
152114
Hom.:
2167
Cov.:
32
AF XY:
0.162
AC XY:
12081
AN XY:
74350
show subpopulations
African (AFR)
AF:
0.140
AC:
5798
AN:
41492
American (AMR)
AF:
0.208
AC:
3181
AN:
15288
Ashkenazi Jewish (ASJ)
AF:
0.324
AC:
1124
AN:
3470
East Asian (EAS)
AF:
0.357
AC:
1842
AN:
5162
South Asian (SAS)
AF:
0.133
AC:
639
AN:
4816
European-Finnish (FIN)
AF:
0.150
AC:
1583
AN:
10582
Middle Eastern (MID)
AF:
0.229
AC:
67
AN:
292
European-Non Finnish (NFE)
AF:
0.133
AC:
9074
AN:
67996
Other (OTH)
AF:
0.173
AC:
364
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1002
2004
3007
4009
5011
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
254
508
762
1016
1270
<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:
0.164
Hom.:
690
Bravo
AF:
0.160
Asia WGS
AF:
0.196
AC:
683
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
2.5
DANN
Benign
0.19
PhyloP100
0.079

Splicing

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

Publications

Other links and lift over

dbSNP: rs12647316; hg19: chr4-111649251; API