rs2826473
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000669643.1(LINC00320):n.1116C>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 0.0629 in 152,150 control chromosomes in the GnomAD database, including 337 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 0.063 ( 337 hom., cov: 32)
Consequence
LINC00320
ENST00000669643.1 non_coding_transcript_exon
ENST00000669643.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.15
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=-1.0).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LINC00320 | ENST00000669643.1 | n.1116C>G | non_coding_transcript_exon_variant | 8/8 | |||||
LINC00320 | ENST00000655781.1 | n.142-7687C>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0629 AC: 9557AN: 152032Hom.: 335 Cov.: 32
GnomAD3 genomes
?
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9557
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152032
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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: 0.0629 AC: 9570AN: 152150Hom.: 337 Cov.: 32 AF XY: 0.0635 AC XY: 4722AN XY: 74394
GnomAD4 genome
?
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AC:
9570
AN:
152150
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Cov.:
32
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4722
AN XY:
74394
Gnomad4 AFR
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Asia WGS
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AC:
339
AN:
3466
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