chr6-40431883-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_020737.3(LRFN2):c.1231G>C(p.Gly411Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000747 in 1,607,148 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_020737.3 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 |
---|---|---|---|---|---|---|---|
LRFN2 | NM_020737.3 | c.1231G>C | p.Gly411Arg | missense_variant | 2/3 | ENST00000338305.7 | |
LRFN2 | XM_011514762.3 | c.1231G>C | p.Gly411Arg | missense_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRFN2 | ENST00000338305.7 | c.1231G>C | p.Gly411Arg | missense_variant | 2/3 | 1 | NM_020737.3 | P1 | |
LRFN2 | ENST00000700335.1 | c.1231G>C | p.Gly411Arg | missense_variant | 3/4 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152236Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000406 AC: 1AN: 246386Hom.: 0 AF XY: 0.00000752 AC XY: 1AN XY: 132946
GnomAD4 exome AF: 0.00000756 AC: 11AN: 1454912Hom.: 0 Cov.: 35 AF XY: 0.00000692 AC XY: 5AN XY: 722824
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152236Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 17, 2023 | The c.1231G>C (p.G411R) alteration is located in exon 2 (coding exon 1) of the LRFN2 gene. This alteration results from a G to C substitution at nucleotide position 1231, causing the glycine (G) at amino acid position 411 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2024 | LRFN2: PM2, BP4 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at