rs6686134

Positions:

• chr1-45912596-A-G
• chr1-45912596-A-T

Variant summary

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

The NM_015112.3(MAST2):​c.500+30201A>G 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 151,998 control chromosomes in the GnomAD database, including 15,265 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 (15265 hom., cov: 32)
• Consequence: MAST2 NM_015112.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.211

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAST2	NM_015112.3	c.500+30201A>G		intron_variant		ENST00000361297.7	NP_055927.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAST2	ENST00000361297.7	c.500+30201A>G		intron_variant		1	NM_015112.3	ENSP00000354671
MAST2	ENST00000470809.1	n.470-4743A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67690 AN: 151880 Hom.: 15280 Cov.: 32

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.377

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: 67670 AN: 151998 Hom.: 15265 Cov.: 32 AF XY: 0.446 AC XY: 33121 AN XY: 74274

Gnomad4 AFR AF: 0.418

Gnomad4 AMR AF: 0.488

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.629

Gnomad4 SAS AF: 0.446

Gnomad4 FIN AF: 0.412

Gnomad4 NFE AF: 0.442

Gnomad4 OTH AF: 0.435

Alfa AF: 0.352 Hom.: 1300

Bravo AF: 0.449

Asia WGS AF: 0.520 AC: 1806 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.60

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: rs6686134; hg19: chr1-46378268;