rs2832270

Variant summary

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

The NR_027072.2(LINC00189):​n.767+27951G>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 0.143 in 152,160 control chromosomes in the GnomAD database, including 2,185 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 0.14 ( 2185 hom., cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

LINC00189
NR_027072.2 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.118
Variant links:
Genes affected
LINC00189 (HGNC:18461): (long intergenic non-protein coding RNA 189)
BACH1 (HGNC:935): (BTB domain and CNC homolog 1) This gene encodes a transcription factor that belongs to the cap'n'collar type of basic region leucine zipper factor family (CNC-bZip). The encoded protein contains broad complex, tramtrack, bric-a-brac/poxvirus and zinc finger (BTB/POZ) domains, which is atypical of CNC-bZip family members. These BTB/POZ domains facilitate protein-protein interactions and formation of homo- and/or hetero-oligomers. When this encoded protein forms a heterodimer with MafK, it functions as a repressor of Maf recognition element (MARE) and transcription is repressed. Multiple alternatively spliced transcript variants have been identified for this gene. [provided by RefSeq, May 2009]

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=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LINC00189NR_027072.2 linkuse as main transcriptn.767+27951G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LINC00189ENST00000447125.5 linkuse as main transcriptn.561+27951G>A intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.143
AC:
21743
AN:
152042
Hom.:
2169
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.285
Gnomad AMI
AF:
0.00220
Gnomad AMR
AF:
0.0832
Gnomad ASJ
AF:
0.130
Gnomad EAS
AF:
0.0636
Gnomad SAS
AF:
0.0615
Gnomad FIN
AF:
0.0695
Gnomad MID
AF:
0.0949
Gnomad NFE
AF:
0.0967
Gnomad OTH
AF:
0.136
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
4
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
2
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
GnomAD4 genome
AF:
0.143
AC:
21779
AN:
152160
Hom.:
2185
Cov.:
32
AF XY:
0.139
AC XY:
10361
AN XY:
74394
show subpopulations
Gnomad4 AFR
AF:
0.285
Gnomad4 AMR
AF:
0.0830
Gnomad4 ASJ
AF:
0.130
Gnomad4 EAS
AF:
0.0633
Gnomad4 SAS
AF:
0.0614
Gnomad4 FIN
AF:
0.0695
Gnomad4 NFE
AF:
0.0967
Gnomad4 OTH
AF:
0.135
Alfa
AF:
0.103
Hom.:
554
Bravo
AF:
0.152
Asia WGS
AF:
0.0810
AC:
286
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.30
DANN
Benign
0.36

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: rs2832270; hg19: chr21-30594532; API