chr11-63468419-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001146729.2(PLAAT5):c.392T>C(p.Ile131Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00029 in 1,614,058 control chromosomes in the GnomAD database, including 1 homozygotes. 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_001146729.2 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLAAT5 | NM_001146729.2 | c.392T>C | p.Ile131Thr | missense_variant | 4/6 | ENST00000540857.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLAAT5 | ENST00000540857.6 | c.392T>C | p.Ile131Thr | missense_variant | 4/6 | 1 | NM_001146729.2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000184 AC: 28AN: 152220Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000995 AC: 25AN: 251380Hom.: 0 AF XY: 0.000110 AC XY: 15AN XY: 135858
GnomAD4 exome AF: 0.000301 AC: 440AN: 1461838Hom.: 1 Cov.: 30 AF XY: 0.000285 AC XY: 207AN XY: 727220
GnomAD4 genome ? AF: 0.000184 AC: 28AN: 152220Hom.: 0 Cov.: 31 AF XY: 0.000175 AC XY: 13AN XY: 74372
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 20, 2023 | The c.422T>C (p.I141T) alteration is located in exon 4 (coding exon 4) of the HRASLS5 gene. This alteration results from a T to C substitution at nucleotide position 422, causing the isoleucine (I) at amino acid position 141 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