chr5-177489394-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_005451.5(PDLIM7):c.868C>T(p.Arg290Trp) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000159 in 1,570,450 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005451.5 missense, splice_region
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 |
---|---|---|---|---|---|---|---|
PDLIM7 | NM_005451.5 | c.868C>T | p.Arg290Trp | missense_variant, splice_region_variant | 9/13 | ENST00000355841.7 | |
PDLIM7 | NM_203352.3 | c.766C>T | p.Arg256Trp | missense_variant, splice_region_variant | 9/13 | ||
PDLIM7 | NR_103804.2 | n.1155C>T | splice_region_variant, non_coding_transcript_exon_variant | 9/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDLIM7 | ENST00000355841.7 | c.868C>T | p.Arg290Trp | missense_variant, splice_region_variant | 9/13 | 1 | NM_005451.5 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152184Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.0000106 AC: 15AN: 1418266Hom.: 0 Cov.: 30 AF XY: 0.0000114 AC XY: 8AN XY: 701012
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152184Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 19, 2024 | The c.868C>T (p.R290W) alteration is located in exon 9 (coding exon 8) of the PDLIM7 gene. This alteration results from a C to T substitution at nucleotide position 868, causing the arginine (R) at amino acid position 290 to be replaced by a tryptophan (W). 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