rs9839841
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_015150.2(RFTN1):c.146-4014G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 152,110 control chromosomes in the GnomAD database, including 3,001 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 0.19 ( 3001 hom., cov: 31)
Consequence
RFTN1
NM_015150.2 intron
NM_015150.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.387
Publications
5 publications found
Genes affected
RFTN1 (HGNC:30278): (raftlin, lipid raft linker 1) Enables double-stranded RNA binding activity. Involved in B cell receptor signaling pathway; membrane raft assembly; and positive regulation of growth rate. Acts upstream of or within dsRNA transport; response to exogenous dsRNA; and toll-like receptor 3 signaling pathway. Located in endosome; membrane raft; and plasma membrane. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.82).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.188 AC: 28543AN: 151992Hom.: 2992 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
28543
AN:
151992
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.188 AC: 28587AN: 152110Hom.: 3001 Cov.: 31 AF XY: 0.187 AC XY: 13945AN XY: 74376 show subpopulations
GnomAD4 genome
AF:
AC:
28587
AN:
152110
Hom.:
Cov.:
31
AF XY:
AC XY:
13945
AN XY:
74376
show subpopulations
African (AFR)
AF:
AC:
10635
AN:
41464
American (AMR)
AF:
AC:
3296
AN:
15280
Ashkenazi Jewish (ASJ)
AF:
AC:
411
AN:
3462
East Asian (EAS)
AF:
AC:
1160
AN:
5176
South Asian (SAS)
AF:
AC:
420
AN:
4828
European-Finnish (FIN)
AF:
AC:
1390
AN:
10596
Middle Eastern (MID)
AF:
AC:
46
AN:
294
European-Non Finnish (NFE)
AF:
AC:
10741
AN:
67986
Other (OTH)
AF:
AC:
392
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1156
2312
3469
4625
5781
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
296
592
888
1184
1480
<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:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
582
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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