chr1-12859817-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_023014.1(PRAMEF2):āc.412T>Cā(p.Cys138Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000684 in 1,607,496 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Likely benign (ā ).
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.412T>C | p.Cys138Arg | missense_variant | 3/4 | ENST00000240189.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRAMEF2 | ENST00000240189.2 | c.412T>C | p.Cys138Arg | missense_variant | 3/4 | 1 | NM_023014.1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000663 AC: 1AN: 150782Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00187 AC: 437AN: 233318Hom.: 53 AF XY: 0.00173 AC XY: 220AN XY: 126802
GnomAD4 exome AF: 0.00000686 AC: 10AN: 1456714Hom.: 0 Cov.: 48 AF XY: 0.00000552 AC XY: 4AN XY: 724734
GnomAD4 genome AF: 0.00000663 AC: 1AN: 150782Hom.: 0 Cov.: 32 AF XY: 0.0000136 AC XY: 1AN XY: 73562
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