10-95238079-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_020992.4(PDLIM1):c.836G>A(p.Arg279His) variant causes a missense change. The variant allele was found at a frequency of 0.0000459 in 1,613,832 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020992.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PDLIM1 | ENST00000329399.7 | c.836G>A | p.Arg279His | missense_variant | Exon 7 of 7 | 1 | NM_020992.4 | ENSP00000360305.3 | ||
PDLIM1 | ENST00000477757.5 | n.781G>A | non_coding_transcript_exon_variant | Exon 6 of 6 | 2 | |||||
PDLIM1 | ENST00000492511.1 | n.314G>A | non_coding_transcript_exon_variant | Exon 2 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152124Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 250288Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135358
GnomAD4 exome AF: 0.0000493 AC: 72AN: 1461708Hom.: 0 Cov.: 32 AF XY: 0.0000495 AC XY: 36AN XY: 727122
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152124Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74322
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.836G>A (p.R279H) alteration is located in exon 7 (coding exon 7) of the PDLIM1 gene. This alteration results from a G to A substitution at nucleotide position 836, causing the arginine (R) at amino acid position 279 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