rs2249017
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_146526.1(LINC02471):n.276A>G 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 0.622 in 152,006 control chromosomes in the GnomAD database, including 30,338 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 0.62 ( 30338 hom., cov: 32)
Failed GnomAD Quality Control
Consequence
LINC02471
NR_146526.1 non_coding_transcript_exon
NR_146526.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.838
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 (NFE) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LINC02471 | NR_146526.1 | n.276A>G | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LINC02471 | ENST00000641941.1 | n.231+11075A>G | intron_variant, non_coding_transcript_variant | ||||||
LINC02471 | ENST00000417422.2 | n.270A>G | non_coding_transcript_exon_variant | 2/2 | 3 | ||||
LINC02471 | ENST00000663154.3 | n.364A>G | non_coding_transcript_exon_variant | 2/2 | |||||
LINC02471 | ENST00000669755.1 | n.261A>G | non_coding_transcript_exon_variant | 2/2 |
Frequencies
GnomAD3 genomes ? AF: 0.622 AC: 94482AN: 151888Hom.: 30319 Cov.: 32
GnomAD3 genomes
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GnomAD4 exome Data not reliable, filtered out with message: AC0AC: 0AN: 0Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
GnomAD4 exome
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GnomAD4 genome ? AF: 0.622 AC: 94542AN: 152006Hom.: 30338 Cov.: 32 AF XY: 0.618 AC XY: 45920AN XY: 74292
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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