chr9-137192122-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001128228.3(TPRN):c.2126T>C(p.Leu709Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000868 in 1,613,238 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. L709L) has been classified as Likely benign.
Frequency
Consequence
NM_001128228.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TPRN | NM_001128228.3 | c.2126T>C | p.Leu709Pro | missense_variant | 4/4 | ENST00000409012.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TPRN | ENST00000409012.6 | c.2126T>C | p.Leu709Pro | missense_variant | 4/4 | 1 | NM_001128228.3 | P1 | |
TPRN | ENST00000477345.1 | n.2847T>C | non_coding_transcript_exon_variant | 3/3 | 1 | ||||
TPRN | ENST00000333046.8 | c.1604T>C | p.Leu535Pro | missense_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152214Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 250168Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135608
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1461024Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 726872
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152214Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74372
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 20, 2023 | The c.2126T>C (p.L709P) alteration is located in exon 4 (coding exon 4) of the TPRN gene. This alteration results from a T to C substitution at nucleotide position 2126, causing the leucine (L) at amino acid position 709 to be replaced by a proline (P). 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