rs6701216
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_178351.4(LCE1C):c.-21+551G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 152,070 control chromosomes in the GnomAD database, including 3,781 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 0.21 ( 3781 hom., cov: 32)
Consequence
LCE1C
NM_178351.4 intron
NM_178351.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.835
Genes affected
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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=-0.96).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LCE1C | NM_178351.4 | c.-21+551G>A | intron_variant | ENST00000607093.2 | |||
LCE1C | NM_001276331.2 | c.-21+551G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LCE1C | ENST00000607093.2 | c.-21+551G>A | intron_variant | NM_178351.4 | P1 | ||||
LCE1C | ENST00000606576.1 | c.-21+551G>A | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.210 AC: 31887AN: 151952Hom.: 3759 Cov.: 32
GnomAD3 genomes
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.210 AC: 31947AN: 152070Hom.: 3781 Cov.: 32 AF XY: 0.215 AC XY: 16011AN XY: 74334
GnomAD4 genome
?
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32
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16011
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1207
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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