19-48993916-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM1BP4_ModerateBS2
The NM_006666.3(RUVBL2):c.5C>T(p.Ala2Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,613,940 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006666.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RUVBL2 | NM_006666.3 | c.5C>T | p.Ala2Val | missense_variant | Exon 1 of 15 | ENST00000595090.6 | NP_006657.1 | |
RUVBL2 | NM_001321190.2 | c.-168C>T | 5_prime_UTR_variant | Exon 1 of 15 | NP_001308119.1 | |||
RUVBL2 | NM_001321191.1 | c.-124+14C>T | intron_variant | Intron 1 of 14 | NP_001308120.1 | |||
RUVBL2 | NR_135578.2 | n.30C>T | non_coding_transcript_exon_variant | Exon 1 of 15 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152096Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000803 AC: 2AN: 249022Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135346
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1461844Hom.: 0 Cov.: 32 AF XY: 0.0000206 AC XY: 15AN XY: 727224
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152096Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74282
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.5C>T (p.A2V) alteration is located in exon 1 (coding exon 1) of the RUVBL2 gene. This alteration results from a C to T substitution at nucleotide position 5, causing the alanine (A) at amino acid position 2 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