chr5-144160438-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM1PM2
The NM_030799.9(YIPF5):c.733G>A(p.Ala245Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,613,938 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_030799.9 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
YIPF5 | NM_030799.9 | c.733G>A | p.Ala245Thr | missense_variant | Exon 6 of 6 | ENST00000274496.10 | NP_110426.4 | |
YIPF5 | NM_001024947.4 | c.733G>A | p.Ala245Thr | missense_variant | Exon 6 of 6 | NP_001020118.1 | ||
YIPF5 | NM_001271732.2 | c.571G>A | p.Ala191Thr | missense_variant | Exon 5 of 5 | NP_001258661.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
YIPF5 | ENST00000274496.10 | c.733G>A | p.Ala245Thr | missense_variant | Exon 6 of 6 | 1 | NM_030799.9 | ENSP00000274496.5 | ||
YIPF5 | ENST00000448443.6 | c.733G>A | p.Ala245Thr | missense_variant | Exon 6 of 6 | 1 | ENSP00000397704.2 | |||
YIPF5 | ENST00000513112.5 | c.571G>A | p.Ala191Thr | missense_variant | Exon 5 of 5 | 1 | ENSP00000425422.1 | |||
YIPF5 | ENST00000519064.5 | c.*40G>A | downstream_gene_variant | 2 | ENSP00000429777.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152114Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251330Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135850
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461824Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 727206
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152114Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74304
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.733G>A (p.A245T) alteration is located in exon 6 (coding exon 5) of the YIPF5 gene. This alteration results from a G to A substitution at nucleotide position 733, causing the alanine (A) at amino acid position 245 to be replaced by a threonine (T). 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