rs1389609436
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002916.5(RFC4):c.1016C>T(p.Ala339Val) variant causes a missense change. The variant allele was found at a frequency of 0.00000657 in 152,202 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002916.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RFC4 | NM_002916.5 | c.1016C>T | p.Ala339Val | missense_variant | Exon 11 of 11 | ENST00000296273.7 | NP_002907.1 | |
RFC4 | NM_181573.3 | c.1016C>T | p.Ala339Val | missense_variant | Exon 11 of 11 | NP_853551.1 | ||
EIF4A2 | NM_001967.4 | c.*776G>A | downstream_gene_variant | ENST00000323963.10 | NP_001958.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152202Hom.: 0 Cov.: 32
GnomAD4 exome Cov.: 30
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152202Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1016C>T (p.A339V) alteration is located in exon 11 (coding exon 10) of the RFC4 gene. This alteration results from a C to T substitution at nucleotide position 1016, causing the alanine (A) at amino acid position 339 to be replaced by a valine (V). 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