chr3-169822526-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001080460.3(LRRIQ4):c.605C>G(p.Ala202Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,461,604 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A202V) has been classified as Likely benign.
Frequency
Consequence
NM_001080460.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LRRIQ4 | ENST00000340806.7 | c.605C>G | p.Ala202Gly | missense_variant | Exon 2 of 6 | 5 | NM_001080460.3 | ENSP00000342188.6 | ||
LRRIQ4 | ENST00000691416.1 | c.605C>G | p.Ala202Gly | missense_variant | Exon 2 of 5 | ENSP00000508855.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 249020Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135100
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461604Hom.: 0 Cov.: 33 AF XY: 0.00000275 AC XY: 2AN XY: 727064
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.605C>G (p.A202G) alteration is located in exon 1 (coding exon 1) of the LRRIQ4 gene. This alteration results from a C to G substitution at nucleotide position 605, causing the alanine (A) at amino acid position 202 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