chr1-27882030-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001105556.3(THEMIS2):c.706G>A(p.Ala236Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000479 in 1,461,844 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
THEMIS2 | NM_001105556.3 | c.706G>A | p.Ala236Thr | missense_variant | 4/6 | ENST00000373921.8 | NP_001099026.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
THEMIS2 | ENST00000373921.8 | c.706G>A | p.Ala236Thr | missense_variant | 4/6 | 5 | NM_001105556.3 | ENSP00000363031.3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249316Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135332
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461844Hom.: 0 Cov.: 30 AF XY: 0.00000550 AC XY: 4AN XY: 727222
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 14, 2024 | The c.706G>A (p.A236T) alteration is located in exon 4 (coding exon 4) of the THEMIS2 gene. This alteration results from a G to A substitution at nucleotide position 706, causing the alanine (A) at amino acid position 236 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