10-125661967-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001128202.3(TEX36):c.62T>A(p.Ile21Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00113 in 1,552,292 control chromosomes in the GnomAD database, including 1 homozygotes. 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 Uncertain significance (★).
Frequency
Consequence
NM_001128202.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TEX36 | NM_001128202.3 | c.62T>A | p.Ile21Asn | missense_variant | 2/4 | ENST00000368821.4 | |
TEX36 | NM_001318133.2 | c.62T>A | p.Ile21Asn | missense_variant | 2/4 | ||
TEX36 | XM_005269817.5 | c.62T>A | p.Ile21Asn | missense_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TEX36 | ENST00000368821.4 | c.62T>A | p.Ile21Asn | missense_variant | 2/4 | 1 | NM_001128202.3 | P1 | |
TEX36 | ENST00000532135.5 | c.62T>A | p.Ile21Asn | missense_variant | 2/4 | 1 | |||
TEX36 | ENST00000526819.5 | c.62T>A | p.Ile21Asn | missense_variant | 2/4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00103 AC: 157AN: 152114Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000793 AC: 126AN: 158910Hom.: 0 AF XY: 0.000717 AC XY: 60AN XY: 83680
GnomAD4 exome AF: 0.00114 AC: 1603AN: 1400060Hom.: 1 Cov.: 31 AF XY: 0.00111 AC XY: 767AN XY: 690506
GnomAD4 genome AF: 0.00103 AC: 157AN: 152232Hom.: 0 Cov.: 32 AF XY: 0.000820 AC XY: 61AN XY: 74434
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 06, 2021 | The c.62T>A (p.I21N) alteration is located in exon 2 (coding exon 2) of the TEX36 gene. This alteration results from a T to A substitution at nucleotide position 62, causing the isoleucine (I) at amino acid position 21 to be replaced by an asparagine (N). 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