chr12-71578813-G-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_003667.4(LGR5):c.1290G>T(p.Ser430=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000836 in 1,607,154 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0046 ( 6 hom., cov: 32)
Exomes 𝑓: 0.00045 ( 1 hom. )
Consequence
LGR5
NM_003667.4 synonymous
NM_003667.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.974
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 -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.66).
BP6
?
Variant 12-71578813-G-T is Benign according to our data. Variant chr12-71578813-G-T is described in ClinVar as [Benign]. Clinvar id is 779529.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.974 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00455 (693/152202) while in subpopulation AFR AF= 0.0161 (667/41532). AF 95% confidence interval is 0.0151. There are 6 homozygotes in gnomad4. There are 324 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 6 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LGR5 | NM_003667.4 | c.1290G>T | p.Ser430= | synonymous_variant | 15/18 | ENST00000266674.10 | |
LOC124902963 | XR_007063365.1 | n.126-1782C>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LGR5 | ENST00000266674.10 | c.1290G>T | p.Ser430= | synonymous_variant | 15/18 | 1 | NM_003667.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00453 AC: 689AN: 152084Hom.: 6 Cov.: 32
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GnomAD3 exomes AF: 0.00110 AC: 272AN: 246920Hom.: 1 AF XY: 0.000764 AC XY: 102AN XY: 133438
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GnomAD4 exome AF: 0.000447 AC: 651AN: 1454952Hom.: 1 Cov.: 30 AF XY: 0.000384 AC XY: 278AN XY: 723586
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 15, 2018 | - - |
Computational 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