7-100575252-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002319.5(LRCH4):c.1907G>A(p.Arg636Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000883 in 1,586,348 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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. R636W) has been classified as Likely benign.
Frequency
Consequence
NM_002319.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000558 AC: 11AN: 196980Hom.: 0 AF XY: 0.0000843 AC XY: 9AN XY: 106744
GnomAD4 exome AF: 0.0000879 AC: 126AN: 1434182Hom.: 0 Cov.: 32 AF XY: 0.0000717 AC XY: 51AN XY: 710868
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1907G>A (p.R636Q) alteration is located in exon 18 (coding exon 18) of the LRCH4 gene. This alteration results from a G to A substitution at nucleotide position 1907, causing the arginine (R) at amino acid position 636 to be replaced by a glutamine (Q). 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