ENST00000420364.1:n.767+1595G>A

Variant names:

• chr21-29195855-G-A
• rs9982010
• ENST00000420364.1:n.767+1595G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000420364.1(LINC00189):​n.767+1595G>A variant causes a intron 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 ENST00000420364.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• Publications: 2 publications found

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]

ENSG00000224649 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC00189	NR_027072.2	n.767+1595G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00189	ENST00000420364.1	n.767+1595G>A		intron_variant	Intron 1 of 1	1
BACH1	ENST00000546469.5	c.-297+1595G>A		intron_variant	Intron 1 of 3	3		ENSP00000449383.1
BACH1	ENST00000547141.5	c.-127+1595G>A		intron_variant	Intron 1 of 2	2		ENSP00000448663.1

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

African (AFR) AF: 0.214 AC: 8880 AN: 41476

American (AMR) AF: 0.485 AC: 7422 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2317 AN: 3468

East Asian (EAS) AF: 0.427 AC: 2209 AN: 5170

South Asian (SAS) AF: 0.633 AC: 3050 AN: 4818

European-Finnish (FIN) AF: 0.762 AC: 8072 AN: 10594

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.716 AC: 48680 AN: 67988

Other (OTH) AF: 0.567 AC: 1198 AN: 2114

Alfa AF: 0.609 Hom.: 4096

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
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs9982010; hg19: chr21-30568176;