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GeneBe

3-16316999-A-G

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_015150.2(RFTN1):c.1566T>C(p.Pro522=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00799 in 1,613,964 control chromosomes in the GnomAD database, including 57 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0064 ( 5 hom., cov: 32)
Exomes 𝑓: 0.0082 ( 52 hom. )

Consequence

RFTN1
NM_015150.2 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.92
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]
OXNAD1 (HGNC:25128): (oxidoreductase NAD binding domain containing 1) Predicted to enable oxidoreductase activity. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 3-16316999-A-G is Benign according to our data. Variant chr3-16316999-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2653606.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-1.92 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 5 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RFTN1NM_015150.2 linkuse as main transcriptc.1566T>C p.Pro522= synonymous_variant 10/10 ENST00000334133.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RFTN1ENST00000334133.9 linkuse as main transcriptc.1566T>C p.Pro522= synonymous_variant 10/101 NM_015150.2 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00640
AC:
973
AN:
151962
Hom.:
5
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00121
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00662
Gnomad ASJ
AF:
0.00461
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000415
Gnomad FIN
AF:
0.0179
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00881
Gnomad OTH
AF:
0.00718
GnomAD3 exomes
AF:
0.00674
AC:
1690
AN:
250870
Hom.:
6
AF XY:
0.00671
AC XY:
909
AN XY:
135556
show subpopulations
Gnomad AFR exome
AF:
0.00129
Gnomad AMR exome
AF:
0.00425
Gnomad ASJ exome
AF:
0.00547
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000588
Gnomad FIN exome
AF:
0.0133
Gnomad NFE exome
AF:
0.00988
Gnomad OTH exome
AF:
0.00686
GnomAD4 exome
AF:
0.00815
AC:
11918
AN:
1461884
Hom.:
52
Cov.:
30
AF XY:
0.00781
AC XY:
5680
AN XY:
727246
show subpopulations
Gnomad4 AFR exome
AF:
0.00125
Gnomad4 AMR exome
AF:
0.00503
Gnomad4 ASJ exome
AF:
0.00547
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000638
Gnomad4 FIN exome
AF:
0.0132
Gnomad4 NFE exome
AF:
0.00930
Gnomad4 OTH exome
AF:
0.00639
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00640
AC:
973
AN:
152080
Hom.:
5
Cov.:
32
AF XY:
0.00655
AC XY:
487
AN XY:
74322
show subpopulations
Gnomad4 AFR
AF:
0.00120
Gnomad4 AMR
AF:
0.00661
Gnomad4 ASJ
AF:
0.00461
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000415
Gnomad4 FIN
AF:
0.0179
Gnomad4 NFE
AF:
0.00881
Gnomad4 OTH
AF:
0.00710
Alfa
AF:
0.00745
Hom.:
2
Bravo
AF:
0.00611
Asia WGS
AF:
0.000289
AC:
1
AN:
3478
EpiCase
AF:
0.00889
EpiControl
AF:
0.00919

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenMar 01, 2023RFTN1: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
Cadd
Benign
0.34
Dann
Benign
0.38

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: rs71310334; hg19: chr3-16358506; COSMIC: COSV100490029; COSMIC: COSV100490029; API