chr10-84224504-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001017924.5(LRIT2):c.721C>G(p.Leu241Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000101 in 1,614,084 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_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.721C>G | p.Leu241Val | missense_variant | 2/3 | ENST00000372113.7 | |
LRIT2 | NM_001284223.1 | c.721C>G | p.Leu241Val | missense_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRIT2 | ENST00000372113.7 | c.721C>G | p.Leu241Val | missense_variant | 2/3 | 1 | NM_001017924.5 | P2 | |
LRIT2 | ENST00000538192.5 | c.721C>G | p.Leu241Val | missense_variant | 2/4 | 1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000854 AC: 13AN: 152194Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000835 AC: 21AN: 251468Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135910
GnomAD4 exome AF: 0.000103 AC: 150AN: 1461890Hom.: 0 Cov.: 31 AF XY: 0.000117 AC XY: 85AN XY: 727248
GnomAD4 genome ? AF: 0.0000854 AC: 13AN: 152194Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 26, 2022 | The c.721C>G (p.L241V) alteration is located in exon 2 (coding exon 2) of the LRIT2 gene. This alteration results from a C to G substitution at nucleotide position 721, causing the leucine (L) at amino acid position 241 to be replaced by a valine (V). 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