chr3-37108075-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006309.4(LRRFIP2):c.712G>A(p.Gly238Arg) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.0000942 in 1,613,814 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006309.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRFIP2 | NM_006309.4 | c.712G>A | p.Gly238Arg | missense_variant, splice_region_variant | 13/28 | ENST00000336686.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRFIP2 | ENST00000336686.9 | c.712G>A | p.Gly238Arg | missense_variant, splice_region_variant | 13/28 | 1 | NM_006309.4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000985 AC: 15AN: 152234Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000439 AC: 11AN: 250774Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135542
GnomAD4 exome AF: 0.0000937 AC: 137AN: 1461462Hom.: 0 Cov.: 29 AF XY: 0.000106 AC XY: 77AN XY: 727038
GnomAD4 genome ? AF: 0.0000985 AC: 15AN: 152352Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74502
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 16, 2022 | The c.712G>A (p.G238R) alteration is located in exon 14 (coding exon 12) of the LRRFIP2 gene. This alteration results from a G to A substitution at nucleotide position 712, causing the glycine (G) at amino acid position 238 to be replaced by an arginine (R). 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