13-19464518-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001395978.1(TPTE2):c.679C>T(p.Arg227Cys) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000479 in 1,611,904 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001395978.1 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TPTE2 | NM_001395978.1 | c.679C>T | p.Arg227Cys | missense_variant, splice_region_variant | 13/23 | ENST00000697147.1 | NP_001382907.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TPTE2 | ENST00000697147.1 | c.679C>T | p.Arg227Cys | missense_variant, splice_region_variant | 13/23 | NM_001395978.1 | ENSP00000513136 | P2 |
Frequencies
GnomAD3 genomes AF: 0.000487 AC: 74AN: 152004Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000322 AC: 80AN: 248568Hom.: 0 AF XY: 0.000343 AC XY: 46AN XY: 134306
GnomAD4 exome AF: 0.000478 AC: 698AN: 1459782Hom.: 0 Cov.: 32 AF XY: 0.000446 AC XY: 324AN XY: 726192
GnomAD4 genome AF: 0.000486 AC: 74AN: 152122Hom.: 0 Cov.: 32 AF XY: 0.000444 AC XY: 33AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 16, 2023 | The c.679C>T (p.R227C) alteration is located in exon 11 (coding exon 10) of the TPTE2 gene. This alteration results from a C to T substitution at nucleotide position 679, causing the arginine (R) at amino acid position 227 to be replaced by a cysteine (C). 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