chr2-42668676-G-A

Variant names:

• chr2-42668676-G-A
• rs10865184
• NM_001330442.2:c.702+8814G>A

Variant summary

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

The NM_001330442.2(MTA3):​c.702+8814G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 151,996 control chromosomes in the GnomAD database, including 3,321 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 0.20 (3321 hom., cov: 32)
• Consequence: MTA3 NM_001330442.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140
• Publications: 3 publications found

Genes affected

MTA3 (HGNC:23784): (metastasis associated 1 family member 3) Predicted to enable histone deacetylase binding activity; transcription coactivator activity; and transcription corepressor activity. Involved in negative regulation of transcription, DNA-templated. Located in nucleoplasm. Part of NuRD complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -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 = 0.484 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001330442.2. 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
	MTA3	NM_001330442.2	MANE Select	c.702+8814G>A		intron	N/A	NP_001317371.1
	MTA3	NM_001330443.2		c.702+8814G>A		intron	N/A	NP_001317372.1
	MTA3	NM_001282755.2		c.534+8814G>A		intron	N/A	NP_001269684.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTA3	ENST00000405094.2	TSL:5 MANE Select	c.702+8814G>A		intron	N/A	ENSP00000385823.1
	MTA3	ENST00000406652.5	TSL:1	c.534+8814G>A		intron	N/A	ENSP00000384249.1
	MTA3	ENST00000407270.7	TSL:1	c.702+8814G>A		intron	N/A	ENSP00000385045.3

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30254 AN: 151878 Hom.: 3322 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.199 AC: 30269 AN: 151996 Hom.: 3321 Cov.: 32 AF XY: 0.205 AC XY: 15191 AN XY: 74278

African (AFR) AF: 0.183 AC: 7597 AN: 41478

American (AMR) AF: 0.170 AC: 2600 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 598 AN: 3468

East Asian (EAS) AF: 0.500 AC: 2585 AN: 5166

South Asian (SAS) AF: 0.317 AC: 1523 AN: 4804

European-Finnish (FIN) AF: 0.261 AC: 2748 AN: 10538

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11966 AN: 67968

Other (OTH) AF: 0.214 AC: 451 AN: 2104

Alfa AF: 0.183 Hom.: 8572

Bravo AF: 0.190

Asia WGS AF: 0.405 AC: 1407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.76
PhyloP100		-0.14
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: rs10865184; hg19: chr2-42895816;