rs10865184

chr2-42668676-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MTA3	NM_001330442.2	c.702+8814G>A		intron_variant		ENST00000405094.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTA3	ENST00000405094.2	c.702+8814G>A		intron_variant		5	NM_001330442.2	A1

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

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.500

Gnomad4 SAS AF: 0.317

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.214

Alfa AF: 0.183 Hom.: 5481

Bravo AF: 0.190

Asia WGS AF: 0.405 AC: 1407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.4
Dann	Benign	0.76

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

Publications

LitVar

Other links and lift over

dbSNP: rs10865184; hg19: chr2-42895816;