rs12732188

Positions:

• chr1-45867686-G-A
• chr1-45867686-G-T

Variant summary

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

The NM_015112.3(MAST2):​c.469-14678G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,134 control chromosomes in the GnomAD database, including 1,348 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 0.11 (1348 hom., cov: 32)
• Consequence: MAST2 NM_015112.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0660

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAST2	NM_015112.3	c.469-14678G>A		intron_variant		ENST00000361297.7	NP_055927.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAST2	ENST00000361297.7	c.469-14678G>A		intron_variant		1	NM_015112.3	ENSP00000354671
MAST2	ENST00000470809.1	n.438-14678G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17214 AN: 152016 Hom.: 1349 Cov.: 32

Gnomad AFR AF: 0.0312

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0528

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.113 AC: 17206 AN: 152134 Hom.: 1348 Cov.: 32 AF XY: 0.108 AC XY: 8068 AN XY: 74368

Gnomad4 AFR AF: 0.0311

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.0535

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.127

Alfa AF: 0.150 Hom.: 865

Bravo AF: 0.108

Asia WGS AF: 0.0290 AC: 102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.6
DANN	Benign	0.58

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: rs12732188; hg19: chr1-46333358;