rs2371978
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_183518.1(LRIG3-DT):n.264+23083T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.748 in 152,006 control chromosomes in the GnomAD database, including 44,095 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 0.75 ( 44095 hom., cov: 30)
Consequence
LRIG3-DT
NR_183518.1 intron, non_coding_transcript
NR_183518.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.37
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=-0.89).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRIG3-DT | NR_183518.1 | n.264+23083T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
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Frequencies
GnomAD3 genomes ? AF: 0.749 AC: 113706AN: 151888Hom.: 44089 Cov.: 30
GnomAD3 genomes
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113706
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151888
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30
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.748 AC: 113731AN: 152006Hom.: 44095 Cov.: 30 AF XY: 0.750 AC XY: 55739AN XY: 74300
GnomAD4 genome
?
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AC:
113731
AN:
152006
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Cov.:
30
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55739
AN XY:
74300
Gnomad4 AFR
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Asia WGS
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AC:
2751
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at