NM_015112.3:c.592+1282G>A

Variant names:

• chr1-45960759-G-A
• rs12759880
• NM_015112.3:c.592+1282G>A

Variant summary

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

The NM_015112.3(MAST2):​c.592+1282G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0721 in 152,262 control chromosomes in the GnomAD database, including 568 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 0.072 (568 hom., cov: 32)
• Consequence: MAST2 NM_015112.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.06
• Publications: 3 publications found

Genes affected

MAST2 (HGNC:19035): (microtubule associated serine/threonine kinase 2) Enables phosphatase binding activity. Predicted to be involved in several processes, including peptidyl-serine phosphorylation; regulation of interleukin-12 production; and spermatid differentiation. Predicted to be located in cytoplasm and plasma membrane. Predicted to be active in microtubule cytoskeleton. [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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015112.3. 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
	MAST2	NM_015112.3	MANE Select	c.592+1282G>A		intron	N/A	NP_055927.2
	MAST2	NM_001324320.2		c.592+1282G>A		intron	N/A	NP_001311249.1
	MAST2	NM_001319245.2		c.592+1282G>A		intron	N/A	NP_001306174.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAST2	ENST00000361297.7	TSL:1 MANE Select	c.592+1282G>A		intron	N/A	ENSP00000354671.2
	MAST2	ENST00000674079.1		c.142+1282G>A		intron	N/A	ENSP00000501318.1
	MAST2	ENST00000372008.6	TSL:5	c.247+1282G>A		intron	N/A	ENSP00000361078.2

Frequencies

GnomAD3 genomes AF: 0.0722 AC: 10978 AN: 152144 Hom.: 569 Cov.: 32

Gnomad AFR AF: 0.0210

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0792

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0311

Gnomad FIN AF: 0.0510

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0883

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

GnomAD4 genome AF: 0.0721 AC: 10971 AN: 152262 Hom.: 568 Cov.: 32 AF XY: 0.0690 AC XY: 5136 AN XY: 74448

African (AFR) AF: 0.0210 AC: 872 AN: 41560

American (AMR) AF: 0.0791 AC: 1210 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 639 AN: 3472

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5176

South Asian (SAS) AF: 0.0311 AC: 150 AN: 4824

European-Finnish (FIN) AF: 0.0510 AC: 541 AN: 10602

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7274 AN: 68014

Other (OTH) AF: 0.0879 AC: 186 AN: 2116

Alfa AF: 0.0782 Hom.: 108

Bravo AF: 0.0720

Asia WGS AF: 0.0170 AC: 60 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.7
DANN	Benign	0.43
PhyloP100		3.1
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: rs12759880; hg19: chr1-46426431;