3-156852858-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001004316.3(LEKR1):āc.139A>Gā(p.Met47Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000306 in 1,534,872 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001004316.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152146Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000778 AC: 11AN: 141476Hom.: 0 AF XY: 0.0000264 AC XY: 2AN XY: 75688
GnomAD4 exome AF: 0.0000304 AC: 42AN: 1382608Hom.: 0 Cov.: 29 AF XY: 0.0000352 AC XY: 24AN XY: 682412
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152264Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74446
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.139A>G (p.M47V) alteration is located in exon 3 (coding exon 2) of the LEKR1 gene. This alteration results from a A to G substitution at nucleotide position 139, causing the methionine (M) at amino acid position 47 to be replaced by a valine (V). 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