chr8-144520576-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_014665.4(LRRC14):c.668G>A(p.Arg223His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000437 in 1,600,228 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. R223C) has been classified as Uncertain significance.
Frequency
Consequence
NM_014665.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRC14 | NM_014665.4 | c.668G>A | p.Arg223His | missense_variant | 3/4 | ENST00000292524.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRC14 | ENST00000292524.6 | c.668G>A | p.Arg223His | missense_variant | 3/4 | 1 | NM_014665.4 | P1 | |
LRRC14 | ENST00000529022.5 | c.668G>A | p.Arg223His | missense_variant | 4/5 | 1 | P1 | ||
LRRC14 | ENST00000527730.1 | c.668G>A | p.Arg223His | missense_variant | 3/3 | 2 | |||
LRRC14 | ENST00000531310.1 | n.1123G>A | non_coding_transcript_exon_variant | 2/2 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152166Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.00000833 AC: 2AN: 240234Hom.: 0 AF XY: 0.00000762 AC XY: 1AN XY: 131240
GnomAD4 exome AF: 0.00000207 AC: 3AN: 1448062Hom.: 0 Cov.: 32 AF XY: 0.00000277 AC XY: 2AN XY: 720926
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152166Hom.: 0 Cov.: 34 AF XY: 0.0000269 AC XY: 2AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 24, 2022 | The c.668G>A (p.R223H) alteration is located in exon 3 (coding exon 2) of the LRRC14 gene. This alteration results from a G to A substitution at nucleotide position 668, causing the arginine (R) at amino acid position 223 to be replaced by a histidine (H). 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