chrX-70553405-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_031276.3(TEX11):āc.2300T>Cā(p.Met767Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00000372 in 1,076,535 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M767V) has been classified as Uncertain significance.
Frequency
Consequence
NM_031276.3 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 |
---|---|---|---|---|---|---|---|
TEX11 | NM_031276.3 | c.2300T>C | p.Met767Thr | missense_variant | 27/30 | ENST00000374333.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TEX11 | ENST00000374333.7 | c.2300T>C | p.Met767Thr | missense_variant | 27/30 | 1 | NM_031276.3 | P2 | |
TEX11 | ENST00000344304.3 | c.2345T>C | p.Met782Thr | missense_variant | 26/29 | 5 | A2 | ||
TEX11 | ENST00000395889.6 | c.2345T>C | p.Met782Thr | missense_variant | 28/31 | 2 | A2 | ||
TEX11 | ENST00000374320.6 | c.1370T>C | p.Met457Thr | missense_variant | 16/19 | 2 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD3 exomes AF: 0.00000592 AC: 1AN: 168898Hom.: 0 AF XY: 0.0000181 AC XY: 1AN XY: 55344
GnomAD4 exome AF: 0.00000372 AC: 4AN: 1076535Hom.: 0 Cov.: 25 AF XY: 0.00000291 AC XY: 1AN XY: 343483
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 27, 2022 | The c.2345T>C (p.M782T) alteration is located in exon 28 (coding exon 26) of the TEX11 gene. This alteration results from a T to C substitution at nucleotide position 2345, causing the methionine (M) at amino acid position 782 to be replaced by a threonine (T). 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