rs6429582

Variant names:

• chr1-45856171-T-C
• rs6429582
• NM_015112.3:c.469-26193T>C

Variant summary

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

The NM_015112.3(MAST2):​c.469-26193T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 152,004 control chromosomes in the GnomAD database, including 15,324 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 0.45 (15324 hom., cov: 32)
• Consequence: MAST2 NM_015112.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.759
• Publications: 12 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAST2	NM_015112.3	c.469-26193T>C		intron_variant	Intron 3 of 28	ENST00000361297.7	NP_055927.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAST2	ENST00000361297.7	c.469-26193T>C		intron_variant	Intron 3 of 28	1	NM_015112.3	ENSP00000354671.2
MAST2	ENST00000470809.1	n.438-26193T>C		intron_variant	Intron 3 of 4	3

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67802 AN: 151886 Hom.: 15337 Cov.: 32

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.446 AC: 67786 AN: 152004 Hom.: 15324 Cov.: 32 AF XY: 0.447 AC XY: 33195 AN XY: 74296

African (AFR) AF: 0.422 AC: 17484 AN: 41442

American (AMR) AF: 0.490 AC: 7473 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1619 AN: 3466

East Asian (EAS) AF: 0.620 AC: 3209 AN: 5176

South Asian (SAS) AF: 0.446 AC: 2145 AN: 4810

European-Finnish (FIN) AF: 0.412 AC: 4345 AN: 10550

Middle Eastern (MID) AF: 0.362 AC: 105 AN: 290

European-Non Finnish (NFE) AF: 0.442 AC: 30063 AN: 67992

Other (OTH) AF: 0.436 AC: 919 AN: 2108

Alfa AF: 0.447 Hom.: 20764

Bravo AF: 0.451

Asia WGS AF: 0.522 AC: 1813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	13
DANN	Benign	0.66
PhyloP100		0.76
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: rs6429582; hg19: chr1-46321843; COSMIC: COSV63616884;