1-69938857-A-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001370785.2(LRRC7):c.711+7287A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 150,936 control chromosomes in the GnomAD database, including 23,302 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 0.55 ( 23302 hom., cov: 28)
Consequence
LRRC7
NM_001370785.2 intron
NM_001370785.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.39
Genes affected
LRRC7 (HGNC:18531): (leucine rich repeat containing 7) Predicted to be involved in several processes, including establishment or maintenance of epithelial cell apical/basal polarity; positive regulation of neuron projection development; and receptor clustering. Located in several cellular components, including centrosome; cytosol; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.97).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LRRC7 | NM_001370785.2 | c.711+7287A>T | intron_variant | ENST00000651989.2 | NP_001357714.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LRRC7 | ENST00000651989.2 | c.711+7287A>T | intron_variant | NM_001370785.2 | ENSP00000498937.2 | |||||
LRRC7 | ENST00000415775.2 | c.-809+7287A>T | intron_variant | 1 | ENSP00000394867.2 | |||||
LRRC7 | ENST00000310961.9 | c.612+7287A>T | intron_variant | 5 | ENSP00000309245.4 | |||||
LRRC7 | ENST00000651217.1 | n.627+7287A>T | intron_variant |
Frequencies
GnomAD3 genomes AF: 0.555 AC: 83651AN: 150824Hom.: 23266 Cov.: 28
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.555 AC: 83726AN: 150936Hom.: 23302 Cov.: 28 AF XY: 0.552 AC XY: 40640AN XY: 73682
GnomAD4 genome
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at