NM_001017403.2:c.107C>T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001017403.2(LGR6):c.107C>T(p.Pro36Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000287 in 1,535,712 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001017403.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LGR6 | NM_001017403.2 | c.107C>T | p.Pro36Leu | missense_variant | Exon 1 of 18 | ENST00000367278.8 | NP_001017403.1 | |
LGR6 | XM_047426928.1 | c.107C>T | p.Pro36Leu | missense_variant | Exon 1 of 17 | XP_047282884.1 | ||
LGR6 | XM_047426929.1 | c.107C>T | p.Pro36Leu | missense_variant | Exon 1 of 16 | XP_047282885.1 | ||
LGR6 | XM_047426931.1 | c.107C>T | p.Pro36Leu | missense_variant | Exon 1 of 17 | XP_047282887.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152154Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000905 AC: 15AN: 165810Hom.: 1 AF XY: 0.0000528 AC XY: 5AN XY: 94724
GnomAD4 exome AF: 0.0000296 AC: 41AN: 1383558Hom.: 0 Cov.: 32 AF XY: 0.0000247 AC XY: 17AN XY: 687376
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152154Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.107C>T (p.P36L) alteration is located in exon 1 (coding exon 1) of the LGR6 gene. This alteration results from a C to T substitution at nucleotide position 107, causing the proline (P) at amino acid position 36 to be replaced by a leucine (L). 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