rs705670
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_034016.1(LINC01502):n.171-612C>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 0.358 in 152,148 control chromosomes in the GnomAD database, including 10,310 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 ( 10310 hom., cov: 33)
Consequence
LINC01502
NR_034016.1 intron, non_coding_transcript
NR_034016.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.90
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 (EAS) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LINC01502 | NR_034016.1 | n.171-612C>G | intron_variant, non_coding_transcript_variant | ||||
LINC01502 | NR_034017.1 | n.171-612C>G | intron_variant, non_coding_transcript_variant | ||||
LINC01502 | NR_109814.1 | n.171-612C>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LINC01502 | ENST00000445997.1 | n.145-612C>G | intron_variant, non_coding_transcript_variant | 2 | |||||
LINC01502 | ENST00000447907.5 | n.161-612C>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.358 AC: 54415AN: 152030Hom.: 10295 Cov.: 33
GnomAD3 genomes
?
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54415
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152030
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.358 AC: 54464AN: 152148Hom.: 10310 Cov.: 33 AF XY: 0.360 AC XY: 26753AN XY: 74356
GnomAD4 genome
?
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AC:
54464
AN:
152148
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33
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26753
AN XY:
74356
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1664
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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