NM_001282755.2:c.-141+31469C>T

Variant names:

• chr2-42526723-C-T
• rs12712846
• NM_001282755.2:c.-141+31469C>T

Variant summary

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

The NM_001282755.2(MTA3):​c.-141+31469C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 151,806 control chromosomes in the GnomAD database, including 9,943 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 0.36 (9943 hom., cov: 30)
• Consequence: MTA3 NM_001282755.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• 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=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MTA3	NM_001282755.2	c.-141+31469C>T		intron_variant	Intron 2 of 17		NP_001269684.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MTA3	ENST00000405592.5	c.-141+31469C>T		intron_variant	Intron 2 of 17	2		ENSP00000383973.1

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54590 AN: 151686 Hom.: 9921 Cov.: 30

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.360 AC: 54656 AN: 151806 Hom.: 9943 Cov.: 30 AF XY: 0.360 AC XY: 26671 AN XY: 74164

African (AFR) AF: 0.396 AC: 16380 AN: 41374

American (AMR) AF: 0.317 AC: 4826 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1188 AN: 3464

East Asian (EAS) AF: 0.362 AC: 1858 AN: 5134

South Asian (SAS) AF: 0.398 AC: 1915 AN: 4814

European-Finnish (FIN) AF: 0.384 AC: 4045 AN: 10546

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.343 AC: 23331 AN: 67924

Other (OTH) AF: 0.369 AC: 780 AN: 2112

Alfa AF: 0.344 Hom.: 4789

Bravo AF: 0.356

Asia WGS AF: 0.433 AC: 1505 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.51
DANN	Benign	0.70
PhyloP100		-0.63
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12712846; hg19: chr2-42753863;