rs377411343
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The ENST00000509768.1(PIGG):c.1355C>T(p.Thr452Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000119 in 1,613,656 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. T452T) has been classified as Benign.
Frequency
Consequence
ENST00000509768.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIGG | NM_001127178.3 | c.1614+8C>T | splice_region_variant, intron_variant | ENST00000453061.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIGG | ENST00000453061.7 | c.1614+8C>T | splice_region_variant, intron_variant | 1 | NM_001127178.3 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152182Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000637 AC: 16AN: 251356Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135858
GnomAD4 exome AF: 0.000123 AC: 180AN: 1461474Hom.: 1 Cov.: 32 AF XY: 0.000124 AC XY: 90AN XY: 727080
GnomAD4 genome AF: 0.0000789 AC: 12AN: 152182Hom.: 0 Cov.: 33 AF XY: 0.0000807 AC XY: 6AN XY: 74320
ClinVar
Submissions by phenotype
Intellectual disability, autosomal recessive 53 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at