rs2591961

Variant names:

• chr5-56942770-A-G
• rs2591961
• NM_001297599.2:c.181-3753T>C

Your query was ambiguous. Multiple possible variants found:

• chr5-56942770-A-G
• chr5-56942770-A-T

Variant summary

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

The NM_001297599.2(MIER3):​c.181-3753T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 152,028 control chromosomes in the GnomAD database, including 8,804 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 0.33 (8804 hom., cov: 32)
• Consequence: MIER3 NM_001297599.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.356
• Publications: 17 publications found

Genes affected

MIER3 (HGNC:26678): (MIER family member 3) Predicted to enable histone deacetylase binding activity and transcription corepressor activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Located in nucleoplasm. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000235635 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001297599.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIER3	NM_001297599.2	MANE Select	c.181-3753T>C		intron	N/A	NP_001284528.1
	MIER3	NM_001297598.2		c.196-3753T>C		intron	N/A	NP_001284527.1
	MIER3	NM_152622.5		c.181-3753T>C		intron	N/A	NP_689835.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIER3	ENST00000381199.8	TSL:1 MANE Select	c.181-3753T>C		intron	N/A	ENSP00000370596.3
	MIER3	ENST00000381226.7	TSL:1	c.196-3753T>C		intron	N/A	ENSP00000370624.3
	MIER3	ENST00000381213.7	TSL:1	c.181-3753T>C		intron	N/A	ENSP00000370611.3

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49625 AN: 151910 Hom.: 8799 Cov.: 32

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.327 AC: 49657 AN: 152028 Hom.: 8804 Cov.: 32 AF XY: 0.332 AC XY: 24644 AN XY: 74328

African (AFR) AF: 0.430 AC: 17824 AN: 41440

American (AMR) AF: 0.386 AC: 5893 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 821 AN: 3470

East Asian (EAS) AF: 0.541 AC: 2797 AN: 5168

South Asian (SAS) AF: 0.345 AC: 1666 AN: 4824

European-Finnish (FIN) AF: 0.261 AC: 2762 AN: 10578

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16857 AN: 67966

Other (OTH) AF: 0.307 AC: 648 AN: 2110

Alfa AF: 0.280 Hom.: 3511

Bravo AF: 0.342

Asia WGS AF: 0.407 AC: 1415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.0
DANN	Benign	0.78
PhyloP100		-0.36
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2591961; hg19: chr5-56238597;