12-71578805-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_003667.4(LGR5):c.1282G>A(p.Asp428Asn) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00476 in 1,603,444 control chromosomes in the GnomAD database, including 41 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_003667.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LGR5 | NM_003667.4 | c.1282G>A | p.Asp428Asn | missense_variant, splice_region_variant | 15/18 | ENST00000266674.10 | |
LOC124902963 | XR_007063365.1 | n.126-1774C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LGR5 | ENST00000266674.10 | c.1282G>A | p.Asp428Asn | missense_variant, splice_region_variant | 15/18 | 1 | NM_003667.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00537 AC: 816AN: 152044Hom.: 8 Cov.: 32
GnomAD3 exomes AF: 0.00535 AC: 1305AN: 243990Hom.: 11 AF XY: 0.00535 AC XY: 705AN XY: 131762
GnomAD4 exome AF: 0.00470 AC: 6825AN: 1451282Hom.: 33 Cov.: 30 AF XY: 0.00450 AC XY: 3248AN XY: 721642
GnomAD4 genome AF: 0.00535 AC: 814AN: 152162Hom.: 8 Cov.: 32 AF XY: 0.00648 AC XY: 482AN XY: 74384
ClinVar
Submissions by phenotype
not provided Benign:1
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