rs10496166
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_183884.1(LINC01890):n.431C>T 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 0.249 in 152,126 control chromosomes in the GnomAD database, including 5,746 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 0.25 ( 5746 hom., cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
LINC01890
NR_183884.1 non_coding_transcript_exon
NR_183884.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.424
Genes affected
LINC01890 (HGNC:52709): (long intergenic non-protein coding RNA 1890)
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LINC01890 | NR_183884.1 | n.431C>T | non_coding_transcript_exon_variant | 1/4 | |||
LINC01888 | NR_183895.1 | n.146-605G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LINC01890 | ENST00000655209.1 | n.431C>T | non_coding_transcript_exon_variant | 1/4 | |||||
LINC01888 | ENST00000655763.1 | n.140-605G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.249 AC: 37800AN: 152008Hom.: 5728 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
37800
AN:
152008
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 36Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 20
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
36
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
20
Gnomad4 AMR exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.249 AC: 37868AN: 152126Hom.: 5746 Cov.: 32 AF XY: 0.250 AC XY: 18614AN XY: 74360
GnomAD4 genome
?
AF:
AC:
37868
AN:
152126
Hom.:
Cov.:
32
AF XY:
AC XY:
18614
AN XY:
74360
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1205
AN:
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