rs225537
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_183612.1(LINC02826):n.696+13695A>G 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 0.362 in 151,946 control chromosomes in the GnomAD database, including 11,445 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 0.36 ( 11445 hom., cov: 32)
Consequence
LINC02826
NR_183612.1 intron, non_coding_transcript
NR_183612.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.775
Genes affected
LINC02826 (HGNC:54357): (long intergenic non-protein coding RNA 2826)
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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 = 0.58 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LINC02826 | NR_183612.1 | n.696+13695A>G | intron_variant, non_coding_transcript_variant | ||||
LOC105370058 | XR_945503.2 | n.107+965T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LINC02826 | ENST00000642407.1 | n.511+13695A>G | intron_variant, non_coding_transcript_variant | ||||||
LINC02826 | ENST00000660252.1 | n.2768-29A>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.362 AC: 54971AN: 151828Hom.: 11421 Cov.: 32
GnomAD3 genomes
?
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54971
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151828
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.362 AC: 55035AN: 151946Hom.: 11445 Cov.: 32 AF XY: 0.360 AC XY: 26739AN XY: 74240
GnomAD4 genome
?
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55035
AN:
151946
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32
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26739
AN XY:
74240
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Asia WGS
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853
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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