chr12-71572861-A-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_003667.4(LGR5):c.1148A>G(p.His383Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000451 in 1,613,476 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_003667.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LGR5 | NM_003667.4 | c.1148A>G | p.His383Arg | missense_variant | 13/18 | ENST00000266674.10 | |
LOC105369833 | XR_001749200.2 | n.22-1132T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LGR5 | ENST00000266674.10 | c.1148A>G | p.His383Arg | missense_variant | 13/18 | 1 | NM_003667.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00240 AC: 366AN: 152208Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.000613 AC: 154AN: 251204Hom.: 1 AF XY: 0.000479 AC XY: 65AN XY: 135770
GnomAD4 exome AF: 0.000248 AC: 362AN: 1461150Hom.: 2 Cov.: 29 AF XY: 0.000190 AC XY: 138AN XY: 726948
GnomAD4 genome ? AF: 0.00240 AC: 366AN: 152326Hom.: 3 Cov.: 32 AF XY: 0.00220 AC XY: 164AN XY: 74490
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 08, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at