rs1906493

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000651482.1(LINC00861):​n.366+28487C>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 0.132 in 152,122 control chromosomes in the GnomAD database, including 1,476 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 0.13 ( 1476 hom., cov: 32)

Consequence

LINC00861
ENST00000651482.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0590
Variant links:
Genes affected
LINC00861 (HGNC:45133): (long intergenic non-protein coding RNA 861)

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=-0.85).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.202 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
LINC00861ENST00000651482.1 linkuse as main transcriptn.366+28487C>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.132
AC:
20052
AN:
152004
Hom.:
1479
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.113
Gnomad AMI
AF:
0.186
Gnomad AMR
AF:
0.0892
Gnomad ASJ
AF:
0.132
Gnomad EAS
AF:
0.0628
Gnomad SAS
AF:
0.214
Gnomad FIN
AF:
0.166
Gnomad MID
AF:
0.165
Gnomad NFE
AF:
0.147
Gnomad OTH
AF:
0.120
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.132
AC:
20051
AN:
152122
Hom.:
1476
Cov.:
32
AF XY:
0.134
AC XY:
9946
AN XY:
74346
show subpopulations
Gnomad4 AFR
AF:
0.112
Gnomad4 AMR
AF:
0.0890
Gnomad4 ASJ
AF:
0.132
Gnomad4 EAS
AF:
0.0630
Gnomad4 SAS
AF:
0.213
Gnomad4 FIN
AF:
0.166
Gnomad4 NFE
AF:
0.147
Gnomad4 OTH
AF:
0.120
Alfa
AF:
0.142
Hom.:
1514
Bravo
AF:
0.123
Asia WGS
AF:
0.149
AC:
517
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
0.43
DANN
Benign
0.39

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1906493; hg19: chr8-127092882; API