1-27882421-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001105556.3(THEMIS2):c.1097C>T(p.Thr366Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000726 in 1,611,816 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001105556.3 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 |
---|---|---|---|---|---|---|---|
THEMIS2 | NM_001105556.3 | c.1097C>T | p.Thr366Met | missense_variant | 4/6 | ENST00000373921.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
THEMIS2 | ENST00000373921.8 | c.1097C>T | p.Thr366Met | missense_variant | 4/6 | 5 | NM_001105556.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000125 AC: 19AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000246 AC: 61AN: 248184Hom.: 0 AF XY: 0.000282 AC XY: 38AN XY: 134662
GnomAD4 exome AF: 0.0000678 AC: 99AN: 1459496Hom.: 0 Cov.: 31 AF XY: 0.0000675 AC XY: 49AN XY: 725654
GnomAD4 genome ? AF: 0.000118 AC: 18AN: 152320Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74482
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 11, 2022 | The c.1097C>T (p.T366M) alteration is located in exon 4 (coding exon 4) of the THEMIS2 gene. This alteration results from a C to T substitution at nucleotide position 1097, causing the threonine (T) at amino acid position 366 to be replaced by a methionine (M). 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