rs117010939

Variant names:

• chr19-311911-C-T
• rs117010939
• NM_017550.3:c.918G>A

Your query was ambiguous. Multiple possible variants found:

• chr19-311911-C-T
• chr19-311911-C-G

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4_Moderate BP6_Moderate BP7 BS2

The NM_017550.3(MIER2):​c.918G>A​(p.Glu306Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00247 in 1,614,066 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0022 (2 hom., cov: 33)
  • Exomes 𝑓: 0.0025 (6 hom.)
• Consequence: MIER2 NM_017550.3 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.631
• Publications: 1 publications found

Genes affected

MIER2 (HGNC:29210): (MIER family member 2) Enables histone deacetylase binding activity. Contributes to histone deacetylase activity. Involved in histone deacetylation. Located in cytoplasm and nucleus. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BP6: Variant 19-311911-C-T is Benign according to our data. Variant chr19-311911-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2648841.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=0.631 with no splicing effect.
• BS2: High Homozygotes in GnomAd4 at 2 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017550.3. 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
	MIER2	NM_017550.3	MANE Select	c.918G>A	p.Glu306Glu	synonymous	Exon 10 of 14	NP_060020.1	Q8N344
	MIER2	NM_001387152.1		c.924G>A	p.Glu308Glu	synonymous	Exon 10 of 14	NP_001374081.1
	MIER2	NM_001387153.1		c.918G>A	p.Glu306Glu	synonymous	Exon 10 of 14	NP_001374082.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIER2	ENST00000264819.7	TSL:1 MANE Select	c.918G>A	p.Glu306Glu	synonymous	Exon 10 of 14	ENSP00000264819.3	Q8N344
	MIER2	ENST00000931432.1		c.825G>A	p.Glu275Glu	synonymous	Exon 9 of 13	ENSP00000601491.1
	MIER2	ENST00000871288.1		c.792G>A	p.Glu264Glu	synonymous	Exon 9 of 13	ENSP00000541347.1

Frequencies

GnomAD3 genomes AF: 0.00217 AC: 331 AN: 152210 Hom.: 2 Cov.: 33

Gnomad AFR AF: 0.000555

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00589

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000188

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00312

Gnomad OTH AF: 0.00143

GnomAD2 exomes AF: 0.00162 AC: 407 AN: 251170 AF XY: 0.00156

Gnomad AFR exome AF: 0.000369

Gnomad AMR exome AF: 0.00211

Gnomad ASJ exome AF: 0.000398

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.000416

Gnomad NFE exome AF: 0.00262

Gnomad OTH exome AF: 0.00196

GnomAD4 exome AF: 0.00250 AC: 3655 AN: 1461738 Hom.: 6 Cov.: 32 AF XY: 0.00239 AC XY: 1741 AN XY: 727190

African (AFR) AF: 0.000329 AC: 11 AN: 33476

American (AMR) AF: 0.00217 AC: 97 AN: 44714

Ashkenazi Jewish (ASJ) AF: 0.000689 AC: 18 AN: 26124

East Asian (EAS) AF: 0.00 AC: 0 AN: 39696

South Asian (SAS) AF: 0.000313 AC: 27 AN: 86258

European-Finnish (FIN) AF: 0.000581 AC: 31 AN: 53402

Middle Eastern (MID) AF: 0.00173 AC: 10 AN: 5768

European-Non Finnish (NFE) AF: 0.00301 AC: 3352 AN: 1111922

Other (OTH) AF: 0.00181 AC: 109 AN: 60378

GnomAD4 genome AF: 0.00217 AC: 331 AN: 152328 Hom.: 2 Cov.: 33 AF XY: 0.00235 AC XY: 175 AN XY: 74480

African (AFR) AF: 0.000553 AC: 23 AN: 41570

American (AMR) AF: 0.00588 AC: 90 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.000288 AC: 1 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5174

South Asian (SAS) AF: 0.00 AC: 0 AN: 4832

European-Finnish (FIN) AF: 0.000188 AC: 2 AN: 10624

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00312 AC: 212 AN: 68028

Other (OTH) AF: 0.00142 AC: 3 AN: 2114

Alfa AF: 0.00201 Hom.: 1

Bravo AF: 0.00209

Asia WGS AF: 0.000577 AC: 2 AN: 3478

EpiCase AF: 0.00256

EpiControl AF: 0.00273

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	8.0
DANN	Benign	0.91
PhyloP100		0.63
Mutation Taster		=100/0	polymorphism

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: rs117010939; hg19: chr19-311911;