chr10-84222132-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.1441G>A(p.Ala481Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000547 in 1,609,140 control chromosomes in the GnomAD database, including 1 homozygotes. 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
Genome browser will be placed here
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.1441G>A | p.Ala481Thr | missense_variant | 3/3 | ENST00000372113.7 | |
LRIT2 | NM_001284223.1 | c.1471G>A | p.Ala491Thr | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRIT2 | ENST00000372113.7 | c.1441G>A | p.Ala481Thr | missense_variant | 3/3 | 1 | NM_001017924.5 | P2 | |
LRIT2 | ENST00000538192.5 | c.1471G>A | p.Ala491Thr | missense_variant | 4/4 | 1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152230Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000802 AC: 20AN: 249352Hom.: 0 AF XY: 0.0000816 AC XY: 11AN XY: 134858
GnomAD4 exome AF: 0.0000556 AC: 81AN: 1456910Hom.: 1 Cov.: 36 AF XY: 0.0000691 AC XY: 50AN XY: 723696
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152230Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74372
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 28, 2022 | The c.1441G>A (p.A481T) 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 1441, causing the alanine (A) at amino acid position 481 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