chr1-161118018-C-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_012394.4(PFDN2):c.9G>T(p.Glu3Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,611,712 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_012394.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PFDN2 | NM_012394.4 | c.9G>T | p.Glu3Asp | missense_variant | 1/4 | ENST00000368010.4 | |
PFDN2 | XM_011509624.4 | c.-185G>T | 5_prime_UTR_variant | 1/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PFDN2 | ENST00000368010.4 | c.9G>T | p.Glu3Asp | missense_variant | 1/4 | 1 | NM_012394.4 | P1 | |
PFDN2 | ENST00000468311.1 | n.38G>T | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152258Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000487 AC: 12AN: 246474Hom.: 0 AF XY: 0.0000224 AC XY: 3AN XY: 133850
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1459454Hom.: 0 Cov.: 33 AF XY: 0.0000165 AC XY: 12AN XY: 726004
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152258Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74390
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 26, 2022 | The c.9G>T (p.E3D) alteration is located in exon 1 (coding exon 1) of the PFDN2 gene. This alteration results from a G to T substitution at nucleotide position 9, causing the glutamic acid (E) at amino acid position 3 to be replaced by an aspartic acid (D). 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