5-179550595-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_025158.5(RUFY1):c.26C>T(p.Ala9Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000335 in 1,344,370 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_025158.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RUFY1 | ENST00000319449.9 | c.26C>T | p.Ala9Val | missense_variant | Exon 1 of 18 | 1 | NM_025158.5 | ENSP00000325594.4 | ||
RUFY1 | ENST00000393448.6 | n.-242C>T | upstream_gene_variant | 1 | ENSP00000377094.2 | |||||
RUFY1 | ENST00000502984.5 | c.-245C>T | upstream_gene_variant | 3 | ENSP00000425533.1 |
Frequencies
GnomAD3 genomes AF: 0.0000415 AC: 5AN: 120550Hom.: 0 Cov.: 35
GnomAD3 exomes AF: 0.0000151 AC: 1AN: 66276Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 38826
GnomAD4 exome AF: 0.0000327 AC: 40AN: 1223820Hom.: 0 Cov.: 35 AF XY: 0.0000383 AC XY: 23AN XY: 601228
GnomAD4 genome AF: 0.0000415 AC: 5AN: 120550Hom.: 0 Cov.: 35 AF XY: 0.0000339 AC XY: 2AN XY: 58918
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.26C>T (p.A9V) alteration is located in exon 1 (coding exon 1) of the RUFY1 gene. This alteration results from a C to T substitution at nucleotide position 26, causing the alanine (A) at amino acid position 9 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