rs1902249

Variant summary

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

The ENST00000295049.9(RFTN2):​c.140-9966A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 151,956 control chromosomes in the GnomAD database, including 35,574 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 0.68 ( 35574 hom., cov: 31)

Consequence

RFTN2
ENST00000295049.9 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.738
Variant links:
Genes affected
RFTN2 (HGNC:26402): (raftlin family member 2) Predicted to act upstream of or within dsRNA transport and response to exogenous dsRNA. Predicted to be located in plasma membrane. [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=-0.96).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.731 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
RFTN2NM_144629.3 linkuse as main transcriptc.140-9966A>G intron_variant ENST00000295049.9 NP_653230.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
RFTN2ENST00000295049.9 linkuse as main transcriptc.140-9966A>G intron_variant 1 NM_144629.3 ENSP00000295049 P1
RFTN2ENST00000429081.1 linkuse as main transcriptc.140-9966A>G intron_variant 4 ENSP00000398128

Frequencies

GnomAD3 genomes
AF:
0.681
AC:
103397
AN:
151838
Hom.:
35550
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.738
Gnomad AMI
AF:
0.714
Gnomad AMR
AF:
0.642
Gnomad ASJ
AF:
0.753
Gnomad EAS
AF:
0.474
Gnomad SAS
AF:
0.655
Gnomad FIN
AF:
0.586
Gnomad MID
AF:
0.848
Gnomad NFE
AF:
0.681
Gnomad OTH
AF:
0.714
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.681
AC:
103472
AN:
151956
Hom.:
35574
Cov.:
31
AF XY:
0.677
AC XY:
50306
AN XY:
74278
show subpopulations
Gnomad4 AFR
AF:
0.738
Gnomad4 AMR
AF:
0.641
Gnomad4 ASJ
AF:
0.753
Gnomad4 EAS
AF:
0.475
Gnomad4 SAS
AF:
0.656
Gnomad4 FIN
AF:
0.586
Gnomad4 NFE
AF:
0.681
Gnomad4 OTH
AF:
0.714
Alfa
AF:
0.683
Hom.:
16853
Bravo
AF:
0.686
Asia WGS
AF:
0.587
AC:
2042
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
1.1
DANN
Benign
0.51

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: rs1902249; hg19: chr2-198521356; API