X-70629688-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_031276.3(TEX11):c.1531T>C(p.Ser511Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000016 in 1,189,580 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 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 (★).
Frequency
Consequence
NM_031276.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TEX11 | NM_031276.3 | c.1531T>C | p.Ser511Pro | missense_variant | 18/30 | ENST00000374333.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TEX11 | ENST00000374333.7 | c.1531T>C | p.Ser511Pro | missense_variant | 18/30 | 1 | NM_031276.3 | P2 | |
TEX11 | ENST00000344304.3 | c.1576T>C | p.Ser526Pro | missense_variant | 17/29 | 5 | A2 | ||
TEX11 | ENST00000395889.6 | c.1576T>C | p.Ser526Pro | missense_variant | 19/31 | 2 | A2 | ||
TEX11 | ENST00000374320.6 | c.601T>C | p.Ser201Pro | missense_variant | 7/19 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000901 AC: 1AN: 110936Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33128
GnomAD4 exome AF: 0.0000167 AC: 18AN: 1078644Hom.: 0 Cov.: 26 AF XY: 0.0000115 AC XY: 4AN XY: 346500
GnomAD4 genome ? AF: 0.00000901 AC: 1AN: 110936Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33128
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 16, 2023 | The c.1576T>C (p.S526P) alteration is located in exon 19 (coding exon 17) of the TEX11 gene. This alteration results from a T to C substitution at nucleotide position 1576, causing the serine (S) at amino acid position 526 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