rs7275620

Variant names:

• chr21-29516557-G-A
• rs7275620
• ENST00000422809.5:c.472-65755G>A

Your query was ambiguous. Multiple possible variants found:

• chr21-29516557-G-A
• chr21-29516557-G-T

Variant summary

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

The ENST00000468059.1(BACH1):​c.325-81013G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.036 in 152,266 control chromosomes in the GnomAD database, including 131 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 0.036 (131 hom., cov: 32)
• Consequence: BACH1 ENST00000468059.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190

Genes affected

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BACH1	ENST00000422809.5	c.472-65755G>A		intron_variant	Intron 2 of 4	5		ENSP00000416569.1
BACH1	ENST00000468059.1	c.325-81013G>A		intron_variant	Intron 2 of 3	3		ENSP00000470673.1

Frequencies

GnomAD3 genomes AF: 0.0358 AC: 5452 AN: 152148 Hom.: 131 Cov.: 32

Gnomad AFR AF: 0.0328

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0676

Gnomad ASJ AF: 0.00634

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.0414

Gnomad FIN AF: 0.0313

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0265

Gnomad OTH AF: 0.0315

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

GnomAD4 genome AF: 0.0360 AC: 5475 AN: 152266 Hom.: 131 Cov.: 32 AF XY: 0.0377 AC XY: 2808 AN XY: 74454

Gnomad4 AFR AF: 0.0330

Gnomad4 AMR AF: 0.0675

Gnomad4 ASJ AF: 0.00634

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.0419

Gnomad4 FIN AF: 0.0313

Gnomad4 NFE AF: 0.0265

Gnomad4 OTH AF: 0.0341

Alfa AF: 0.0286 Hom.: 126

Bravo AF: 0.0383

Asia WGS AF: 0.108 AC: 375 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	0.58
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7275620; hg19: chr21-30888877;