chr1-13262706-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001013407.5(PRAMEF5):c.1026A>T(p.Gln342His) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 10/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar.
Frequency
Consequence
NM_001013407.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRAMEF5 | NM_001013407.5 | c.1026A>T | p.Gln342His | missense_variant | 4/4 | ENST00000622421.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRAMEF5 | ENST00000622421.3 | c.1026A>T | p.Gln342His | missense_variant | 4/4 | 1 | NM_001013407.5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 2
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000857 AC: 4AN: 466486Hom.: 0 Cov.: 5 AF XY: 0.00000830 AC XY: 2AN XY: 241070
GnomAD4 genome Cov.: 2
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 28, 2023 | The c.1026A>T (p.Q342H) alteration is located in exon 4 (coding exon 3) of the PRAMEF5 gene. This alteration results from a A to T substitution at nucleotide position 1026, causing the glutamine (Q) at amino acid position 342 to be replaced by a histidine (H). 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
Publications
No publications associated with this variant yet.