rs140984555
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_031276.3(TEX11):c.2047G>A(p.Ala683Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000291 in 1,202,574 control chromosomes in the GnomAD database, including 1 homozygotes. There are 81 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
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 | UniProt |
---|---|---|---|---|---|---|---|
TEX11 | NM_031276.3 | c.2047G>A | p.Ala683Thr | missense_variant | 24/30 | ENST00000374333.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TEX11 | ENST00000374333.7 | c.2047G>A | p.Ala683Thr | missense_variant | 24/30 | 1 | NM_031276.3 | P2 | |
TEX11 | ENST00000344304.3 | c.2092G>A | p.Ala698Thr | missense_variant | 23/29 | 5 | A2 | ||
TEX11 | ENST00000395889.6 | c.2092G>A | p.Ala698Thr | missense_variant | 25/31 | 2 | A2 | ||
TEX11 | ENST00000374320.6 | c.1117G>A | p.Ala373Thr | missense_variant | 13/19 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00167 AC: 187AN: 111978Hom.: 1 Cov.: 23 AF XY: 0.00149 AC XY: 51AN XY: 34164
GnomAD3 exomes AF: 0.000362 AC: 65AN: 179744Hom.: 0 AF XY: 0.000186 AC XY: 12AN XY: 64392
GnomAD4 exome AF: 0.000149 AC: 163AN: 1090544Hom.: 0 Cov.: 27 AF XY: 0.0000842 AC XY: 30AN XY: 356502
GnomAD4 genome ? AF: 0.00167 AC: 187AN: 112030Hom.: 1 Cov.: 23 AF XY: 0.00149 AC XY: 51AN XY: 34226
ClinVar
Submissions by phenotype
not specified Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Feb 21, 2024 | The p.Ala698Thr variant in TEX11 is classified as likely benign because it has been identified in 0.55% (315/57191) of African chromosomes including 72 hemizygotes and 1 homozygote by gnomAD (http://gnomad.broadinstitute.org, v.4.0.0). In addition, computational prediction tools predict that this variant does not impact the protein. ACMG/AMP Criteria applied: BS1, BP4. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Mendelics | May 04, 2022 | - - |
Spermatogenic failure, X-linked, 2 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | May 28, 2015 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 27, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at