9-137192133-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_001128228.3(TPRN):c.2115C>T(p.Ser705Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000607 in 1,613,436 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001128228.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TPRN | ENST00000409012.6 | c.2115C>T | p.Ser705Ser | synonymous_variant | Exon 4 of 4 | 1 | NM_001128228.3 | ENSP00000387100.4 | ||
TPRN | ENST00000477345.1 | n.2836C>T | non_coding_transcript_exon_variant | Exon 3 of 3 | 1 | |||||
TPRN | ENST00000333046.8 | c.1593C>T | p.Ser531Ser | synonymous_variant | Exon 3 of 3 | 2 | ENSP00000327617.4 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152234Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000399 AC: 10AN: 250408Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135706
GnomAD4 exome AF: 0.0000650 AC: 95AN: 1461202Hom.: 0 Cov.: 31 AF XY: 0.0000812 AC XY: 59AN XY: 726930
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152234Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74372
ClinVar
Submissions by phenotype
not provided Benign:2
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This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at