chr2-151428862-A-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_018151.5(RIF1):ā€‹c.865A>Gā€‹(p.Ile289Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000359 in 1,392,676 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā˜…).

Frequency

Genomes: not found (cov: 32)
Exomes š‘“: 0.0000036 ( 0 hom. )

Consequence

RIF1
NM_018151.5 missense

Scores

1
18

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.71
Variant links:
Genes affected
RIF1 (HGNC:23207): (replication timing regulatory factor 1) This gene encodes a protein that shares homology with the yeast teleomere binding protein, Rap1 interacting factor 1. This protein localizes to aberrant telomeres may be involved in DNA repair. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Apr 2010]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.100710005).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RIF1NM_018151.5 linkuse as main transcriptc.865A>G p.Ile289Val missense_variant 9/36 ENST00000444746.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RIF1ENST00000444746.7 linkuse as main transcriptc.865A>G p.Ile289Val missense_variant 9/361 NM_018151.5 P2Q5UIP0-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.00000797
AC:
2
AN:
251014
Hom.:
0
AF XY:
0.00000737
AC XY:
1
AN XY:
135730
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000579
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000359
AC:
5
AN:
1392676
Hom.:
0
Cov.:
25
AF XY:
0.00000143
AC XY:
1
AN XY:
697018
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000896
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
9.53e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32
ExAC
AF:
0.00000824
AC:
1

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsMar 24, 2023The c.865A>G (p.I289V) alteration is located in exon 9 (coding exon 8) of the RIF1 gene. This alteration results from a A to G substitution at nucleotide position 865, causing the isoleucine (I) at amino acid position 289 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.094
BayesDel_addAF
Benign
-0.23
T
BayesDel_noAF
Benign
-0.40
CADD
Benign
14
DANN
Benign
0.90
DEOGEN2
Benign
0.13
T;.;.;T;.
Eigen
Benign
-0.42
Eigen_PC
Benign
-0.24
FATHMM_MKL
Uncertain
0.86
D
LIST_S2
Benign
0.83
.;.;.;T;T
M_CAP
Benign
0.0052
T
MetaRNN
Benign
0.10
T;T;T;T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
0.055
N;N;N;N;N
MutationTaster
Benign
0.98
D;D;D;D;D;D
PrimateAI
Benign
0.48
T
PROVEAN
Benign
-0.37
N;N;N;N;N
REVEL
Benign
0.038
Sift
Benign
0.34
T;T;T;T;T
Sift4G
Benign
0.43
T;T;T;T;T
Polyphen
0.37
B;P;P;B;P
Vest4
0.17
MutPred
0.28
Gain of methylation at K290 (P = 0.0505);Gain of methylation at K290 (P = 0.0505);Gain of methylation at K290 (P = 0.0505);Gain of methylation at K290 (P = 0.0505);Gain of methylation at K290 (P = 0.0505);
MVP
0.24
MPC
0.047
ClinPred
0.081
T
GERP RS
3.5
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.021
gMVP
0.14

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: rs753438017; hg19: chr2-152285376; API