chrX-115123183-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_020871.4(LRCH2):c.1859G>A(p.Arg620His) variant causes a missense change. The variant allele was found at a frequency of 0.000086 in 1,197,782 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 34 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020871.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LRCH2 | NM_020871.4 | c.1859G>A | p.Arg620His | missense_variant | Exon 18 of 21 | ENST00000317135.13 | NP_065922.3 | |
LRCH2 | NM_001243963.2 | c.1808G>A | p.Arg603His | missense_variant | Exon 17 of 20 | NP_001230892.1 | ||
LRCH2 | XM_006724724.4 | c.1838G>A | p.Arg613His | missense_variant | Exon 18 of 21 | XP_006724787.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LRCH2 | ENST00000317135.13 | c.1859G>A | p.Arg620His | missense_variant | Exon 18 of 21 | 1 | NM_020871.4 | ENSP00000325091.8 | ||
LRCH2 | ENST00000538422.2 | c.1808G>A | p.Arg603His | missense_variant | Exon 17 of 20 | 1 | ENSP00000439366.1 |
Frequencies
GnomAD3 genomes AF: 0.0000719 AC: 8AN: 111217Hom.: 0 Cov.: 23 AF XY: 0.0000897 AC XY: 3AN XY: 33455
GnomAD3 exomes AF: 0.0000410 AC: 7AN: 170774Hom.: 0 AF XY: 0.0000520 AC XY: 3AN XY: 57738
GnomAD4 exome AF: 0.0000874 AC: 95AN: 1086565Hom.: 0 Cov.: 29 AF XY: 0.0000879 AC XY: 31AN XY: 352751
GnomAD4 genome AF: 0.0000719 AC: 8AN: 111217Hom.: 0 Cov.: 23 AF XY: 0.0000897 AC XY: 3AN XY: 33455
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1859G>A (p.R620H) alteration is located in exon 18 (coding exon 18) of the LRCH2 gene. This alteration results from a G to A substitution at nucleotide position 1859, causing the arginine (R) at amino acid position 620 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