chr1-12859724-G-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_023014.1(PRAMEF2):c.319G>T(p.Asp107Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000113 in 1,606,560 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D107E) 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 -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRAMEF2 | NM_023014.1 | c.319G>T | p.Asp107Tyr | missense_variant | 3/4 | ENST00000240189.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRAMEF2 | ENST00000240189.2 | c.319G>T | p.Asp107Tyr | missense_variant | 3/4 | 1 | NM_023014.1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000464 AC: 7AN: 150966Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000282 AC: 7AN: 248242Hom.: 0 AF XY: 0.0000297 AC XY: 4AN XY: 134858
GnomAD4 exome AF: 0.000120 AC: 174AN: 1455594Hom.: 5 Cov.: 34 AF XY: 0.000124 AC XY: 90AN XY: 724200
GnomAD4 genome AF: 0.0000464 AC: 7AN: 150966Hom.: 0 Cov.: 33 AF XY: 0.0000678 AC XY: 5AN XY: 73696
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2022 | The c.319G>T (p.D107Y) alteration is located in exon 3 (coding exon 2) of the PRAMEF2 gene. This alteration results from a G to T substitution at nucleotide position 319, causing the aspartic acid (D) at amino acid position 107 to be replaced by a tyrosine (Y). 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