GeneBe

rs4260611

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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 0.31 ( 12203 hom., cov: 19)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.229

Publications

2 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=-0.95).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.407 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:
0.309
AC:
38024
AN:
122998
Hom.:
12187
Cov.:
19
show subpopulations
Gnomad AFR
AF:
0.231
Gnomad AMI
AF:
0.386
Gnomad AMR
AF:
0.415
Gnomad ASJ
AF:
0.276
Gnomad EAS
AF:
0.389
Gnomad SAS
AF:
0.295
Gnomad FIN
AF:
0.396
Gnomad MID
AF:
0.183
Gnomad NFE
AF:
0.326
Gnomad OTH
AF:
0.277
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.309
AC:
38066
AN:
123060
Hom.:
12203
Cov.:
19
AF XY:
0.313
AC XY:
18341
AN XY:
58564
show subpopulations
African (AFR)
AF:
0.232
AC:
8378
AN:
36182
American (AMR)
AF:
0.416
AC:
4962
AN:
11922
Ashkenazi Jewish (ASJ)
AF:
0.276
AC:
811
AN:
2936
East Asian (EAS)
AF:
0.393
AC:
504
AN:
1284
South Asian (SAS)
AF:
0.295
AC:
761
AN:
2584
European-Finnish (FIN)
AF:
0.396
AC:
2744
AN:
6926
Middle Eastern (MID)
AF:
0.202
AC:
48
AN:
238
European-Non Finnish (NFE)
AF:
0.326
AC:
19122
AN:
58582
Other (OTH)
AF:
0.273
AC:
466
AN:
1706
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
705
1409
2114
2818
3523
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
298
596
894
1192
1490
<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:
0.270
Hom.:
982
Asia WGS
AF:
0.247
AC:
466
AN:
1886

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
2.3
DANN
Benign
0.33
PhyloP100
0.23

Splicing

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

Publications

Other links and lift over

dbSNP: rs4260611; hg19: chr4-69384606; API