chr2-151414845-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018151.5(RIF1):c.206C>T(p.Ser69Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000082 in 1,610,056 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018151.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RIF1 | NM_018151.5 | c.206C>T | p.Ser69Leu | missense_variant | 4/36 | ENST00000444746.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RIF1 | ENST00000444746.7 | c.206C>T | p.Ser69Leu | missense_variant | 4/36 | 1 | NM_018151.5 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152078Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000140 AC: 35AN: 249490Hom.: 0 AF XY: 0.000148 AC XY: 20AN XY: 134724
GnomAD4 exome AF: 0.0000878 AC: 128AN: 1457860Hom.: 0 Cov.: 29 AF XY: 0.0000966 AC XY: 70AN XY: 724984
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152196Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74422
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 11, 2021 | The c.206C>T (p.S69L) alteration is located in exon 4 (coding exon 3) of the RIF1 gene. This alteration results from a C to T substitution at nucleotide position 206, causing the serine (S) at amino acid position 69 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at