chr4-134200414-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001114734.2(PABPC4L):c.606T>A(p.Asp202Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000141 in 1,555,822 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict 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. D202V) has been classified as Uncertain significance.
Frequency
Consequence
NM_001114734.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PABPC4L | NM_001114734.2 | c.606T>A | p.Asp202Glu | missense_variant | 2/2 | ENST00000421491.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PABPC4L | ENST00000421491.4 | c.606T>A | p.Asp202Glu | missense_variant | 2/2 | 3 | NM_001114734.2 | P1 | |
ENST00000658435.1 | n.412-96897T>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152064Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000625 AC: 1AN: 159930Hom.: 0 AF XY: 0.0000118 AC XY: 1AN XY: 84674
GnomAD4 exome AF: 0.0000142 AC: 20AN: 1403758Hom.: 0 Cov.: 53 AF XY: 0.0000130 AC XY: 9AN XY: 692790
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152064Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74268
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 13, 2023 | The c.780T>A (p.D260E) alteration is located in exon 2 (coding exon 1) of the PABPC4L gene. This alteration results from a T to A substitution at nucleotide position 780, causing the aspartic acid (D) at amino acid position 260 to be replaced by a glutamic acid (E). 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