rs12141934

chr1-45887660-A-G

Variant summary

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

The NM_015112.3(MAST2):c.500+5265A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0904 in 152,228 control chromosomes in the GnomAD database, including 853 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 0.090 (853 hom., cov: 32)
• Consequence: MAST2 NM_015112.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171

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=-0.47).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAST2	NM_015112.3	c.500+5265A>G		intron_variant		ENST00000361297.7
LOC105378694	XR_001738038.2	n.2394+7875T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAST2	ENST00000361297.7	c.500+5265A>G		intron_variant		1	NM_015112.3
MAST2	ENST00000470809.1	n.469+5265A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0905 AC: 13765 AN: 152110 Hom.: 854 Cov.: 32

Gnomad AFR AF: 0.0251

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.0799

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0719

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.0904 AC: 13765 AN: 152228 Hom.: 853 Cov.: 32 AF XY: 0.0864 AC XY: 6433 AN XY: 74424

Gnomad4 AFR AF: 0.0250

Gnomad4 AMR AF: 0.0797

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.0719

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.108

Alfa AF: 0.128 Hom.: 1715

Bravo AF: 0.0869

Asia WGS AF: 0.0390 AC: 136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
Cadd	Benign	13
Dann	Benign	0.82

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: rs12141934; hg19: chr1-46353332;