chr1-187209585-C-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_126347.1(LINC01036):n.106-93881C>A 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 0.834 in 150,820 control chromosomes in the GnomAD database, including 52,546 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 0.83 ( 52546 hom., cov: 27)
Consequence
LINC01036
NR_126347.1 intron, non_coding_transcript
NR_126347.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.153
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=-0.97).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LINC01036 | NR_126347.1 | n.106-93881C>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LINC01036 | ENST00000643891.1 | n.804-117336C>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.834 AC: 125691AN: 150714Hom.: 52490 Cov.: 27
GnomAD3 genomes
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125691
AN:
150714
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Cov.:
27
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.834 AC: 125801AN: 150820Hom.: 52546 Cov.: 27 AF XY: 0.837 AC XY: 61635AN XY: 73622
GnomAD4 genome
?
AF:
AC:
125801
AN:
150820
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Cov.:
27
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61635
AN XY:
73622
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2720
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3468
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