rs17325887
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_001370785.2(LRRC7):c.303+97T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0285 in 978,586 control chromosomes in the GnomAD database, including 491 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 0.031 ( 78 hom., cov: 32)
Exomes 𝑓: 0.028 ( 413 hom. )
Consequence
LRRC7
NM_001370785.2 intron
NM_001370785.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.00300
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=-0.86).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0307 (4673/152136) while in subpopulation AFR AF= 0.046 (1912/41534). AF 95% confidence interval is 0.0443. There are 78 homozygotes in gnomad4. There are 2239 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 4673 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRC7 | NM_001370785.2 | c.303+97T>C | intron_variant | ENST00000651989.2 | |||
LOC124904199 | XR_007066167.1 | n.264+55A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRC7 | ENST00000651989.2 | c.303+97T>C | intron_variant | NM_001370785.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0308 AC: 4678AN: 152018Hom.: 79 Cov.: 32
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GnomAD4 exome AF: 0.0280 AC: 23179AN: 826450Hom.: 413 AF XY: 0.0284 AC XY: 12071AN XY: 424584
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GnomAD4 genome ? AF: 0.0307 AC: 4673AN: 152136Hom.: 78 Cov.: 32 AF XY: 0.0301 AC XY: 2239AN XY: 74394
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3478
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