rs183266
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_169510.1(LOC105370579):n.1951G>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 0.869 in 152,034 control chromosomes in the GnomAD database, including 57,524 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 0.87 ( 57523 hom., cov: 31)
Exomes 𝑓: 0.75 ( 1 hom. )
Consequence
LOC105370579
NR_169510.1 non_coding_transcript_exon
NR_169510.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.23
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=-0.86).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.887 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC105370579 | NR_169510.1 | n.1951G>T | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENST00000693076.1 | n.1626G>T | non_coding_transcript_exon_variant | 2/2 |
Frequencies
GnomAD3 genomes ? AF: 0.869 AC: 132083AN: 151912Hom.: 57495 Cov.: 31
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31
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GnomAD4 exome AF: 0.750 AC: 3AN: 4Hom.: 1 AF XY: 0.750 AC XY: 3AN XY: 4
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GnomAD4 genome ? AF: 0.869 AC: 132167AN: 152030Hom.: 57523 Cov.: 31 AF XY: 0.867 AC XY: 64465AN XY: 74332
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ClinVar
Not reported inComputational scores
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Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at