chr10-84222056-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001017924.5(LRIT2):c.1517C>G(p.Ala506Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000838 in 1,610,952 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
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRIT2 | NM_001017924.5 | c.1517C>G | p.Ala506Gly | missense_variant | 3/3 | ENST00000372113.7 | |
LRIT2 | NM_001284223.1 | c.1547C>G | p.Ala516Gly | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRIT2 | ENST00000372113.7 | c.1517C>G | p.Ala506Gly | missense_variant | 3/3 | 1 | NM_001017924.5 | P2 | |
LRIT2 | ENST00000538192.5 | c.1547C>G | p.Ala516Gly | missense_variant | 4/4 | 1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000414 AC: 63AN: 152208Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000929 AC: 23AN: 247542Hom.: 0 AF XY: 0.0000821 AC XY: 11AN XY: 133920
GnomAD4 exome AF: 0.0000480 AC: 70AN: 1458626Hom.: 0 Cov.: 36 AF XY: 0.0000483 AC XY: 35AN XY: 725204
GnomAD4 genome ? AF: 0.000427 AC: 65AN: 152326Hom.: 0 Cov.: 33 AF XY: 0.000416 AC XY: 31AN XY: 74488
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 27, 2022 | The c.1517C>G (p.A506G) alteration is located in exon 3 (coding exon 3) of the LRIT2 gene. This alteration results from a C to G substitution at nucleotide position 1517, causing the alanine (A) at amino acid position 506 to be replaced by a glycine (G). 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