chr10-84224422-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001017924.5(LRIT2):c.803A>T(p.Gln268Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001017924.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRIT2 | NM_001017924.5 | c.803A>T | p.Gln268Leu | missense_variant | 2/3 | ENST00000372113.7 | |
LRIT2 | NM_001284223.1 | c.803A>T | p.Gln268Leu | missense_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRIT2 | ENST00000372113.7 | c.803A>T | p.Gln268Leu | missense_variant | 2/3 | 1 | NM_001017924.5 | P2 | |
LRIT2 | ENST00000538192.5 | c.803A>T | p.Gln268Leu | missense_variant | 2/4 | 1 | A2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 24, 2023 | The c.803A>T (p.Q268L) alteration is located in exon 2 (coding exon 2) of the LRIT2 gene. This alteration results from a A to T substitution at nucleotide position 803, causing the glutamine (Q) at amino acid position 268 to be replaced by a leucine (L). 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
Publications
No publications associated with this variant yet.