chr3-46521558-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024512.5(LRRC2):c.1030G>A(p.Val344Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,612,280 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_024512.5 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 |
---|---|---|---|---|---|---|---|
LRRC2 | NM_024512.5 | c.1030G>A | p.Val344Ile | missense_variant | 8/9 | ENST00000395905.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRC2 | ENST00000395905.8 | c.1030G>A | p.Val344Ile | missense_variant | 8/9 | 1 | NM_024512.5 | P1 | |
LRRC2 | ENST00000296144.3 | c.1030G>A | p.Val344Ile | missense_variant | 8/9 | 1 | P1 | ||
LRRC2 | ENST00000682605.1 | c.1030G>A | p.Val344Ile | missense_variant | 8/9 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000840 AC: 21AN: 249912Hom.: 0 AF XY: 0.0000962 AC XY: 13AN XY: 135140
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1460004Hom.: 0 Cov.: 29 AF XY: 0.0000179 AC XY: 13AN XY: 726378
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152276Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74468
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 11, 2022 | The c.1030G>A (p.V344I) alteration is located in exon 8 (coding exon 7) of the LRRC2 gene. This alteration results from a G to A substitution at nucleotide position 1030, causing the valine (V) at amino acid position 344 to be replaced by an isoleucine (I). 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