chr1-12859826-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate
The NM_023014.1(PRAMEF2):āc.421A>Gā(p.Thr141Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/23 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T141K) has been classified as Uncertain significance.
Frequency
Consequence
NM_023014.1 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 |
---|---|---|---|---|---|---|---|
PRAMEF2 | NM_023014.1 | c.421A>G | p.Thr141Ala | missense_variant | 3/4 | ENST00000240189.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRAMEF2 | ENST00000240189.2 | c.421A>G | p.Thr141Ala | missense_variant | 3/4 | 1 | NM_023014.1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 1443AN: 146444Hom.: 15 Cov.: 32 FAILED QC
GnomAD3 exomes AF: 0.000636 AC: 157AN: 246734Hom.: 5 AF XY: 0.000585 AC XY: 78AN XY: 133350
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00328 AC: 4589AN: 1397474Hom.: 857 Cov.: 58 AF XY: 0.00349 AC XY: 2425AN XY: 693958
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00984 AC: 1442AN: 146542Hom.: 15 Cov.: 32 AF XY: 0.00999 AC XY: 714AN XY: 71466
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2024 | PRAMEF2: BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at