10-84222065-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001017924.5(LRIT2):c.1508G>A(p.Arg503His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000431 in 1,610,570 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LRIT2 | ENST00000372113.7 | c.1508G>A | p.Arg503His | missense_variant | Exon 3 of 3 | 1 | NM_001017924.5 | ENSP00000361185.3 | ||
LRIT2 | ENST00000538192.5 | c.1538G>A | p.Arg513His | missense_variant | Exon 4 of 4 | 1 | ENSP00000438264.1 |
Frequencies
GnomAD3 genomes AF: 0.000335 AC: 51AN: 152210Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000388 AC: 96AN: 247208Hom.: 0 AF XY: 0.000374 AC XY: 50AN XY: 133770
GnomAD4 exome AF: 0.000441 AC: 643AN: 1458242Hom.: 0 Cov.: 36 AF XY: 0.000439 AC XY: 318AN XY: 724956
GnomAD4 genome AF: 0.000335 AC: 51AN: 152328Hom.: 0 Cov.: 33 AF XY: 0.000242 AC XY: 18AN XY: 74486
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1508G>A (p.R503H) alteration is located in exon 3 (coding exon 3) of the LRIT2 gene. This alteration results from a G to A substitution at nucleotide position 1508, causing the arginine (R) at amino acid position 503 to be replaced by a histidine (H). 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