5-177489554-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The ENST00000393551.5(PDLIM7):c.646G>A(p.Gly216Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00143 in 1,610,658 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
ENST00000393551.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDLIM7 | NM_005451.5 | c.708G>A | p.Pro236= | synonymous_variant | 9/13 | ENST00000355841.7 | |
PDLIM7 | NM_203352.3 | c.606G>A | p.Pro202= | synonymous_variant | 9/13 | ||
PDLIM7 | NR_103804.2 | n.995G>A | non_coding_transcript_exon_variant | 9/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDLIM7 | ENST00000355841.7 | c.708G>A | p.Pro236= | synonymous_variant | 9/13 | 1 | NM_005451.5 | P3 |
Frequencies
GnomAD3 genomes AF: 0.00718 AC: 1093AN: 152192Hom.: 15 Cov.: 34
GnomAD3 exomes AF: 0.00183 AC: 441AN: 241024Hom.: 5 AF XY: 0.00134 AC XY: 176AN XY: 131144
GnomAD4 exome AF: 0.000832 AC: 1213AN: 1458348Hom.: 10 Cov.: 34 AF XY: 0.000732 AC XY: 531AN XY: 725396
GnomAD4 genome AF: 0.00720 AC: 1097AN: 152310Hom.: 15 Cov.: 34 AF XY: 0.00697 AC XY: 519AN XY: 74456
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at