rs433632
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_131192.1(LINC01671):n.779T>C 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 0.734 in 151,920 control chromosomes in the GnomAD database, including 41,875 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 0.73 ( 41866 hom., cov: 33)
Exomes 𝑓: 0.81 ( 9 hom. )
Consequence
LINC01671
NR_131192.1 non_coding_transcript_exon
NR_131192.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.90
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=-1.02).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LINC01671 | NR_131192.1 | n.779T>C | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LINC01671 | ENST00000419628.2 | n.778T>C | non_coding_transcript_exon_variant | 2/2 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.734 AC: 111447AN: 151776Hom.: 41829 Cov.: 33
GnomAD3 genomes
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GnomAD4 exome AF: 0.808 AC: 21AN: 26Hom.: 9 Cov.: 0 AF XY: 0.778 AC XY: 14AN XY: 18
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GnomAD4 genome ? AF: 0.734 AC: 111547AN: 151894Hom.: 41866 Cov.: 33 AF XY: 0.727 AC XY: 53930AN XY: 74226
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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