chr19-362273-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_016585.5(THEG):āc.1067C>Gā(p.Pro356Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000138 in 1,445,204 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_016585.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
THEG | NM_016585.5 | c.1067C>G | p.Pro356Arg | missense_variant | 8/8 | ENST00000342640.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPMAP2 | ENST00000342640.9 | c.1067C>G | p.Pro356Arg | missense_variant | 8/8 | 1 | NM_016585.5 | A2 | |
SPMAP2 | ENST00000346878.3 | c.995C>G | p.Pro332Arg | missense_variant | 7/7 | 2 | P2 | ||
SPMAP2 | ENST00000530711.3 | c.400C>G | p.Pro134Ala | missense_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152132Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.00000411 AC: 1AN: 243230Hom.: 0 AF XY: 0.00000762 AC XY: 1AN XY: 131186
GnomAD4 exome AF: 0.0000138 AC: 20AN: 1445204Hom.: 0 Cov.: 30 AF XY: 0.0000209 AC XY: 15AN XY: 716692
GnomAD4 genome Cov.: 30
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 31, 2024 | The c.1067C>G (p.P356R) alteration is located in exon 8 (coding exon 8) of the THEG gene. This alteration results from a C to G substitution at nucleotide position 1067, causing the proline (P) at amino acid position 356 to be replaced by an arginine (R). 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