rs31685
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_109891.1(LINC01847):n.3691+9706C>T 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 0.751 in 152,124 control chromosomes in the GnomAD database, including 43,991 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 ( 43991 hom., cov: 32)
Consequence
LINC01847
NR_109891.1 intron, non_coding_transcript
NR_109891.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.342
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=-0.91).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.923 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LINC01847 | NR_109891.1 | n.3691+9706C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LINC01847 | ENST00000522627.1 | n.3691+9706C>T | intron_variant, non_coding_transcript_variant | 1 | |||||
LINC01847 | ENST00000641163.1 | n.252+10692C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.751 AC: 114089AN: 152006Hom.: 43930 Cov.: 32
GnomAD3 genomes
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152006
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32
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GnomAD4 genome ? AF: 0.751 AC: 114205AN: 152124Hom.: 43991 Cov.: 32 AF XY: 0.749 AC XY: 55723AN XY: 74378
GnomAD4 genome
?
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AC:
114205
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152124
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32
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55723
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74378
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2801
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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