rs10890361

chr1-45880562-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015112.3(MAST2):c.469-1802T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 152,044 control chromosomes in the GnomAD database, including 15,276 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 (15276 hom., cov: 32)
• Consequence: MAST2 NM_015112.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.443

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]

LOC105378694 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• 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/exons	MANE	UniProt
MAST2	NM_015112.3	c.469-1802T>A		intron_variant		ENST00000361297.7
LOC105378694	XR_001738038.2	n.2395-3723A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAST2	ENST00000361297.7	c.469-1802T>A		intron_variant		1	NM_015112.3
MAST2	ENST00000470809.1	n.438-1802T>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67719 AN: 151924 Hom.: 15291 Cov.: 32

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.381

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.445 AC: 67699 AN: 152044 Hom.: 15276 Cov.: 32 AF XY: 0.446 AC XY: 33148 AN XY: 74312

Gnomad4 AFR AF: 0.419

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.620

Gnomad4 SAS AF: 0.446

Gnomad4 FIN AF: 0.413

Gnomad4 NFE AF: 0.442

Gnomad4 OTH AF: 0.435

Alfa AF: 0.441 Hom.: 1840

Bravo AF: 0.449

Asia WGS AF: 0.518 AC: 1797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	6.5
Dann	Benign	0.80

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: rs10890361; hg19: chr1-46346234; COSMIC: COSV63616938;