rs689953

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015150.2(RFTN1):​c.1030+2805G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 149,222 control chromosomes in the GnomAD database, including 20,684 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 0.53 ( 20684 hom., cov: 32)

Consequence

RFTN1
NM_015150.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.156
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.62).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.56 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
RFTN1NM_015150.2 linkuse as main transcriptc.1030+2805G>A intron_variant ENST00000334133.9 NP_055965.1 Q14699Q8N5I0

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
RFTN1ENST00000334133.9 linkuse as main transcriptc.1030+2805G>A intron_variant 1 NM_015150.2 ENSP00000334153.4 Q14699
RFTN1ENST00000432519.5 linkuse as main transcriptc.922+2805G>A intron_variant 1 ENSP00000403926.1 G3XAJ6
RFTN1ENST00000483671.1 linkuse as main transcriptn.309+2805G>A intron_variant 2
ENSG00000287377ENST00000653928.1 linkuse as main transcriptn.348-2408C>T intron_variant

Frequencies

GnomAD3 genomes
AF:
0.526
AC:
78430
AN:
149112
Hom.:
20674
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.536
Gnomad AMI
AF:
0.634
Gnomad AMR
AF:
0.459
Gnomad ASJ
AF:
0.580
Gnomad EAS
AF:
0.350
Gnomad SAS
AF:
0.311
Gnomad FIN
AF:
0.474
Gnomad MID
AF:
0.567
Gnomad NFE
AF:
0.565
Gnomad OTH
AF:
0.561
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.526
AC:
78477
AN:
149222
Hom.:
20684
Cov.:
32
AF XY:
0.517
AC XY:
37435
AN XY:
72458
show subpopulations
Gnomad4 AFR
AF:
0.536
Gnomad4 AMR
AF:
0.459
Gnomad4 ASJ
AF:
0.580
Gnomad4 EAS
AF:
0.350
Gnomad4 SAS
AF:
0.311
Gnomad4 FIN
AF:
0.474
Gnomad4 NFE
AF:
0.565
Gnomad4 OTH
AF:
0.556
Alfa
AF:
0.550
Hom.:
31187
Bravo
AF:
0.519

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.62
CADD
Benign
13
DANN
Benign
0.84

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs689953; hg19: chr3-16408778; API