NM_001077700.3:c.773-45A>T

Variant names:

• chr1-66970763-A-T
• rs4553158
• NM_001077700.3:c.773-45A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001077700.3(MIER1):​c.773-45A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000161 in 1,242,814 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000016 (0 hom.)
• Consequence: MIER1 NM_001077700.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.62
• Publications: 0 publications found

Genes affected

MIER1 (HGNC:29657): (MIER1 transcriptional regulator) This gene encodes a protein that was first identified in Xenopus laevis by its role in a mesoderm induction early response (MIER). The encoded protein functions as a transcriptional regulator. Alternatively spliced transcript variants encode multiple isoforms, some of which lack a C-terminal nuclear localization signal. [provided by RefSeq, May 2013]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001077700.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIER1	NM_001077700.3	MANE Select	c.773-45A>T		intron	N/A	NP_001071168.2
	MIER1	NM_001350530.2		c.884-45A>T		intron	N/A	NP_001337459.1
	MIER1	NM_001146110.2		c.665-45A>T		intron	N/A	NP_001139582.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIER1	ENST00000401041.6	TSL:2 MANE Select	c.773-45A>T		intron	N/A	ENSP00000383820.1
	MIER1	ENST00000357692.6	TSL:1	c.665-45A>T		intron	N/A	ENSP00000350321.2
	MIER1	ENST00000355356.3	TSL:1	c.614-45A>T		intron	N/A	ENSP00000347514.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000161 AC: 2 AN: 1242814 Hom.: 0 Cov.: 17 AF XY: 0.00000325 AC XY: 2 AN XY: 615854

African (AFR) AF: 0.00 AC: 0 AN: 26110

American (AMR) AF: 0.0000844 AC: 2 AN: 23688

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19546

East Asian (EAS) AF: 0.00 AC: 0 AN: 35184

South Asian (SAS) AF: 0.00 AC: 0 AN: 60768

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 49910

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5010

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 970636

Other (OTH) AF: 0.00 AC: 0 AN: 51962

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.068
DANN	Benign	0.30
PhyloP100		-2.6

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: rs4553158; hg19: chr1-67436446;