chr1-12859794-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_023014.1(PRAMEF2):c.389G>A(p.Ser130Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000436 in 1,607,152 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_023014.1 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRAMEF2 | NM_023014.1 | c.389G>A | p.Ser130Asn | missense_variant | 3/4 | ENST00000240189.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRAMEF2 | ENST00000240189.2 | c.389G>A | p.Ser130Asn | missense_variant | 3/4 | 1 | NM_023014.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000663 AC: 1AN: 150838Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 250154Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135288
GnomAD4 exome AF: 0.00000412 AC: 6AN: 1456314Hom.: 1 Cov.: 60 AF XY: 0.00000276 AC XY: 2AN XY: 724528
GnomAD4 genome ? AF: 0.00000663 AC: 1AN: 150838Hom.: 0 Cov.: 32 AF XY: 0.0000136 AC XY: 1AN XY: 73602
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 31, 2023 | The c.389G>A (p.S130N) alteration is located in exon 3 (coding exon 2) of the PRAMEF2 gene. This alteration results from a G to A substitution at nucleotide position 389, causing the serine (S) at amino acid position 130 to be replaced by an asparagine (N). 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