chr1-12941444-C-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001010889.2(PRAMEF6):c.409G>C(p.Asp137His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000132 in 1,370,322 control chromosomes in the GnomAD database, including 6 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_001010889.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRAMEF6 | ENST00000376189.5 | c.409G>C | p.Asp137His | missense_variant | Exon 3 of 4 | 1 | NM_001010889.2 | ENSP00000365360.1 | ||
PRAMEF6 | ENST00000415464.6 | c.409G>C | p.Asp137His | missense_variant | Exon 3 of 4 | 1 | ENSP00000401281.2 |
Frequencies
GnomAD3 genomes AF: 0.0000315 AC: 3AN: 95274Hom.: 1 Cov.: 13
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 250562Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135550
GnomAD4 exome AF: 0.000132 AC: 181AN: 1370322Hom.: 6 Cov.: 32 AF XY: 0.000130 AC XY: 89AN XY: 682380
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000315 AC: 3AN: 95274Hom.: 1 Cov.: 13 AF XY: 0.00 AC XY: 0AN XY: 45694
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.409G>C (p.D137H) alteration is located in exon 3 (coding exon 2) of the PRAMEF6 gene. This alteration results from a G to C substitution at nucleotide position 409, causing the aspartic acid (D) at amino acid position 137 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