X-70609156-G-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_031276.3(TEX11):āc.1814C>Gā(p.Pro605Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000506 in 1,204,361 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 22 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_031276.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TEX11 | NM_031276.3 | c.1814C>G | p.Pro605Arg | missense_variant | 22/30 | ENST00000374333.7 | NP_112566.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TEX11 | ENST00000374333.7 | c.1814C>G | p.Pro605Arg | missense_variant | 22/30 | 1 | NM_031276.3 | ENSP00000363453 | P2 | |
TEX11 | ENST00000344304.3 | c.1859C>G | p.Pro620Arg | missense_variant | 21/29 | 5 | ENSP00000340995 | A2 | ||
TEX11 | ENST00000395889.6 | c.1859C>G | p.Pro620Arg | missense_variant | 23/31 | 2 | ENSP00000379226 | A2 | ||
TEX11 | ENST00000374320.6 | c.884C>G | p.Pro295Arg | missense_variant | 11/19 | 2 | ENSP00000363440 |
Frequencies
GnomAD3 genomes AF: 0.0000624 AC: 7AN: 112191Hom.: 0 Cov.: 23 AF XY: 0.0000873 AC XY: 3AN XY: 34349
GnomAD3 exomes AF: 0.000102 AC: 18AN: 175691Hom.: 0 AF XY: 0.000148 AC XY: 9AN XY: 60753
GnomAD4 exome AF: 0.0000494 AC: 54AN: 1092170Hom.: 0 Cov.: 29 AF XY: 0.0000531 AC XY: 19AN XY: 358110
GnomAD4 genome AF: 0.0000624 AC: 7AN: 112191Hom.: 0 Cov.: 23 AF XY: 0.0000873 AC XY: 3AN XY: 34349
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 25, 2022 | The c.1859C>G (p.P620R) alteration is located in exon 23 (coding exon 21) of the TEX11 gene. This alteration results from a C to G substitution at nucleotide position 1859, causing the proline (P) at amino acid position 620 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