GeneBe

rs3847859

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 0.394 in 152,064 control chromosomes in the GnomAD database, including 12,045 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 0.39 ( 12045 hom., cov: 32)

Consequence

LOC102724178
intragenic

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.143

Publications

8 publications found
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC102724178 n.51899716G>A intragenic_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.394
AC:
59858
AN:
151946
Hom.:
12040
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.430
Gnomad AMI
AF:
0.501
Gnomad AMR
AF:
0.316
Gnomad ASJ
AF:
0.350
Gnomad EAS
AF:
0.349
Gnomad SAS
AF:
0.432
Gnomad FIN
AF:
0.416
Gnomad MID
AF:
0.367
Gnomad NFE
AF:
0.387
Gnomad OTH
AF:
0.403
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.394
AC:
59896
AN:
152064
Hom.:
12045
Cov.:
32
AF XY:
0.395
AC XY:
29393
AN XY:
74328
show subpopulations
African (AFR)
AF:
0.430
AC:
17836
AN:
41460
American (AMR)
AF:
0.316
AC:
4832
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
0.350
AC:
1214
AN:
3472
East Asian (EAS)
AF:
0.349
AC:
1804
AN:
5166
South Asian (SAS)
AF:
0.430
AC:
2070
AN:
4814
European-Finnish (FIN)
AF:
0.416
AC:
4399
AN:
10572
Middle Eastern (MID)
AF:
0.367
AC:
108
AN:
294
European-Non Finnish (NFE)
AF:
0.387
AC:
26333
AN:
67984
Other (OTH)
AF:
0.400
AC:
844
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1867
3734
5601
7468
9335
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
582
1164
1746
2328
2910
<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:
0.384
Hom.:
50667
Bravo
AF:
0.386
Asia WGS
AF:
0.386
AC:
1345
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
3.7
DANN
Benign
0.60
PhyloP100
0.14

Splicing

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

Publications

Other links and lift over

dbSNP: rs3847859; hg19: chr12-52293500; API