rs9982010

chr21-29195855-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_027072.2(LINC00189):n.767+1595G>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 0.543 in 152,130 control chromosomes in the GnomAD database, including 26,249 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 0.54 (26249 hom., cov: 33)
• Consequence: LINC00189 NR_027072.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00189	NR_027072.2	n.767+1595G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00189	ENST00000447125.5	n.561+1595G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.544 AC: 82640 AN: 152012 Hom.: 26249 Cov.: 33

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.762

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.571

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.543 AC: 82658 AN: 152130 Hom.: 26249 Cov.: 33 AF XY: 0.546 AC XY: 40618 AN XY: 74352

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.485

Gnomad4 ASJ AF: 0.668

Gnomad4 EAS AF: 0.427

Gnomad4 SAS AF: 0.633

Gnomad4 FIN AF: 0.762

Gnomad4 NFE AF: 0.716

Gnomad4 OTH AF: 0.567

Alfa AF: 0.625 Hom.: 4073

Bravo AF: 0.506

Asia WGS AF: 0.490 AC: 1706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.3
Dann	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9982010; hg19: chr21-30568176;