chr8-42180297-G-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_000930.5(PLAT):c.1167C>A(p.Val389=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00188 in 1,614,142 control chromosomes in the GnomAD database, including 49 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. V389V) has been classified as Benign.
Frequency
Consequence
NM_000930.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLAT | NM_000930.5 | c.1167C>A | p.Val389= | synonymous_variant | 11/14 | ENST00000220809.9 | |
PLAT | NM_033011.4 | c.1029C>A | p.Val343= | synonymous_variant | 10/13 | ||
PLAT | NM_001319189.2 | c.900C>A | p.Val300= | synonymous_variant | 9/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLAT | ENST00000220809.9 | c.1167C>A | p.Val389= | synonymous_variant | 11/14 | 1 | NM_000930.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0103 AC: 1563AN: 152192Hom.: 27 Cov.: 33
GnomAD3 exomes AF: 0.00261 AC: 657AN: 251492Hom.: 6 AF XY: 0.00181 AC XY: 246AN XY: 135922
GnomAD4 exome AF: 0.00100 AC: 1466AN: 1461832Hom.: 22 Cov.: 33 AF XY: 0.000868 AC XY: 631AN XY: 727216
GnomAD4 genome ? AF: 0.0103 AC: 1567AN: 152310Hom.: 27 Cov.: 33 AF XY: 0.00948 AC XY: 706AN XY: 74484
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