2-1643399-T-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_012293.3(PXDN):c.3921A>T(p.Val1307=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,558 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. V1307V) has been classified as Benign.
Frequency
Consequence
NM_012293.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PXDN | NM_012293.3 | c.3921A>T | p.Val1307= | synonymous_variant | 19/23 | ENST00000252804.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PXDN | ENST00000252804.9 | c.3921A>T | p.Val1307= | synonymous_variant | 19/23 | 1 | NM_012293.3 | P1 | |
PXDN | ENST00000477093.1 | n.563A>T | non_coding_transcript_exon_variant | 3/3 | 4 | ||||
PXDN | ENST00000478155.5 | n.3009A>T | non_coding_transcript_exon_variant | 11/15 | 2 | ||||
PXDN | ENST00000453308.1 | c.75A>T | p.Val25= | synonymous_variant, NMD_transcript_variant | 1/4 | 3 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 248898Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135094
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461558Hom.: 0 Cov.: 67 AF XY: 0.00000275 AC XY: 2AN XY: 727068
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at