rs7307225
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003667.4(LGR5):c.213-36T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 1,551,822 control chromosomes in the GnomAD database, including 9,015 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.093 ( 709 hom., cov: 32)
Exomes 𝑓: 0.11 ( 8306 hom. )
Consequence
LGR5
NM_003667.4 intron
NM_003667.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.218
Genes affected
LGR5 (HGNC:4504): (leucine rich repeat containing G protein-coupled receptor 5) The protein encoded by this gene is a leucine-rich repeat-containing receptor (LGR) and member of the G protein-coupled, 7-transmembrane receptor (GPCR) superfamily. The encoded protein is a receptor for R-spondins and is involved in the canonical Wnt signaling pathway. This protein plays a role in the formation and maintenance of adult intestinal stem cells during postembryonic development. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LGR5 | NM_003667.4 | c.213-36T>C | intron_variant | ENST00000266674.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LGR5 | ENST00000266674.10 | c.213-36T>C | intron_variant | 1 | NM_003667.4 | P1 | |||
LGR5 | ENST00000536515.5 | c.213-36T>C | intron_variant | 1 | |||||
LGR5 | ENST00000540815.2 | c.213-36T>C | intron_variant | 1 | |||||
LGR5 | ENST00000550851.5 | n.310-36T>C | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0934 AC: 14212AN: 152136Hom.: 713 Cov.: 32
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GnomAD3 exomes AF: 0.0875 AC: 21976AN: 251190Hom.: 1125 AF XY: 0.0903 AC XY: 12263AN XY: 135738
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GnomAD4 exome AF: 0.105 AC: 147252AN: 1399568Hom.: 8306 Cov.: 25 AF XY: 0.105 AC XY: 73817AN XY: 700084
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GnomAD4 genome ? AF: 0.0934 AC: 14213AN: 152254Hom.: 709 Cov.: 32 AF XY: 0.0920 AC XY: 6852AN XY: 74440
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at