chr2-99404620-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_016316.4(REV1):c.2869G>A(p.Val957Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,460,330 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_016316.4 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
REV1 | NM_016316.4 | c.2869G>A | p.Val957Ile | missense_variant | 18/23 | ENST00000258428.8 | NP_057400.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
REV1 | ENST00000258428.8 | c.2869G>A | p.Val957Ile | missense_variant | 18/23 | 1 | NM_016316.4 | ENSP00000258428 | P4 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249210Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134712
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460330Hom.: 0 Cov.: 33 AF XY: 0.00000275 AC XY: 2AN XY: 726408
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 26, 2024 | The c.2869G>A (p.V957I) alteration is located in exon 18 (coding exon 17) of the REV1 gene. This alteration results from a G to A substitution at nucleotide position 2869, causing the valine (V) at amino acid position 957 to be replaced by an isoleucine (I). 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