rs12759880

chr1-45960759-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAST2	NM_015112.3	c.592+1282G>A		intron_variant		ENST00000361297.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAST2	ENST00000361297.7	c.592+1282G>A		intron_variant		1	NM_015112.3
MAST2	ENST00000372008.6	c.247+1282G>A		intron_variant		5
MAST2	ENST00000674079.1	c.142+1282G>A		intron_variant				P1
MAST2	ENST00000482881.1	n.92+1282G>A		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.0210

Gnomad4 AMR AF: 0.0791

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0311

Gnomad4 FIN AF: 0.0510

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.0879

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	9.7
Dann	Benign	0.43

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: rs12759880; hg19: chr1-46426431;