rs358806
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_183740.1(LINC02030):n.484-6946A>C 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 0.825 in 152,216 control chromosomes in the GnomAD database, including 52,099 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 0.82 ( 52099 hom., cov: 34)
Consequence
LINC02030
NR_183740.1 intron, non_coding_transcript
NR_183740.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.129
Genes affected
LINC02030 (HGNC:52864): (long intergenic non-protein coding RNA 2030)
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=-0.92).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.89 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LINC02030 | NR_183740.1 | n.484-6946A>C | intron_variant, non_coding_transcript_variant | ||||
LOC124906243 | XR_007095917.1 | n.100-12452T>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LINC02030 | ENST00000654581.1 | n.363-6946A>C | intron_variant, non_coding_transcript_variant | ||||||
LINC02030 | ENST00000662390.1 | n.321-6946A>C | intron_variant, non_coding_transcript_variant | ||||||
LINC02030 | ENST00000670191.1 | n.213-6946A>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.825 AC: 125446AN: 152098Hom.: 52051 Cov.: 34
GnomAD3 genomes
?
AF:
AC:
125446
AN:
152098
Hom.:
Cov.:
34
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.825 AC: 125550AN: 152216Hom.: 52099 Cov.: 34 AF XY: 0.824 AC XY: 61290AN XY: 74404
GnomAD4 genome
?
AF:
AC:
125550
AN:
152216
Hom.:
Cov.:
34
AF XY:
AC XY:
61290
AN XY:
74404
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:
3002
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