rs7262320
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_026885.1(LCDR):n.543G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 152,038 control chromosomes in the GnomAD database, including 3,191 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 0.19 ( 3190 hom., cov: 32)
Exomes 𝑓: 0.40 ( 1 hom. )
Consequence
LCDR
NR_026885.1 non_coding_transcript_exon
NR_026885.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0800
Genes affected
LCDR (HGNC:44308): (lysosome cell death regulator)
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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=-0.81).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LCDR | NR_026885.1 | n.543G>T | non_coding_transcript_exon_variant | 1/1 | |||
LINC00652 | NR_026883.1 | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LCDR | ENST00000609087.2 | n.514G>T | non_coding_transcript_exon_variant | 1/1 | |||||
LINC00652 | ENST00000664962.1 | upstream_gene_variant | |||||||
LINC00652 | ENST00000669396.1 | upstream_gene_variant |
Frequencies
GnomAD3 genomes ? AF: 0.194 AC: 29536AN: 151910Hom.: 3188 Cov.: 32
GnomAD3 genomes
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32
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GnomAD4 exome AF: 0.400 AC: 4AN: 10Hom.: 1 Cov.: 0 AF XY: 0.400 AC XY: 4AN XY: 10
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GnomAD4 genome ? AF: 0.194 AC: 29565AN: 152028Hom.: 3190 Cov.: 32 AF XY: 0.190 AC XY: 14131AN XY: 74284
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at