ENST00000452157.5:n.*2762A>G

Variant names:

• chr5-56921702-T-C
• rs16886496
• ENST00000452157.5:n.*2762A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000452157.5(MIER3):​n.*2762A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0911 in 152,690 control chromosomes in the GnomAD database, including 656 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 0.091 (655 hom., cov: 33)
  • Exomes 𝑓: 0.099 (1 hom.)
• Consequence: MIER3 ENST00000452157.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.826
• Publications: 10 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]

SETD9 (HGNC:28508): (SET domain containing 9) Predicted to enable lysine N-methyltransferase activity. Predicted to be involved in regulation of signal transduction by p53 class mediator. Predicted to be located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIER3	NM_001297599.2	c.*1426A>G		3_prime_UTR_variant	Exon 13 of 13	ENST00000381199.8	NP_001284528.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIER3	ENST00000381199.8	c.*1426A>G		3_prime_UTR_variant	Exon 13 of 13	1	NM_001297599.2	ENSP00000370596.3

Frequencies

GnomAD3 genomes AF: 0.0910 AC: 13846 AN: 152138 Hom.: 655 Cov.: 33

Gnomad AFR AF: 0.0875

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0840

Gnomad ASJ AF: 0.0960

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0827

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0914

Gnomad OTH AF: 0.0991

GnomAD4 exome AF: 0.0991 AC: 43 AN: 434 Hom.: 1 Cov.: 0 AF XY: 0.0885 AC XY: 23 AN XY: 260

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.0967 AC: 41 AN: 424

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 6

Other (OTH) AF: 0.500 AC: 2 AN: 4

GnomAD4 genome AF: 0.0910 AC: 13862 AN: 152256 Hom.: 655 Cov.: 33 AF XY: 0.0918 AC XY: 6837 AN XY: 74452

African (AFR) AF: 0.0876 AC: 3641 AN: 41562

American (AMR) AF: 0.0838 AC: 1283 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0960 AC: 333 AN: 3468

East Asian (EAS) AF: 0.142 AC: 736 AN: 5186

South Asian (SAS) AF: 0.102 AC: 490 AN: 4822

European-Finnish (FIN) AF: 0.0827 AC: 877 AN: 10602

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0915 AC: 6219 AN: 67998

Other (OTH) AF: 0.0981 AC: 207 AN: 2110

Alfa AF: 0.0937 Hom.: 1077

Bravo AF: 0.0922

Asia WGS AF: 0.104 AC: 362 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	12
DANN	Benign	0.83
PhyloP100		0.83
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: rs16886496; hg19: chr5-56217529;