1-45807994-G-A

Variant names:

• chr1-45807994-G-A
• rs10437063
• NM_015112.3:c.177+3922G>A

Variant summary

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

The NM_015112.3(MAST2):​c.177+3922G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 152,090 control chromosomes in the GnomAD database, including 9,185 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 0.34 (9185 hom., cov: 32)
• Consequence: MAST2 NM_015112.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.291
• Publications: 2 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015112.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAST2	NM_015112.3	MANE Select	c.177+3922G>A		intron	N/A	NP_055927.2
	MAST2	NM_001324320.2		c.177+3922G>A		intron	N/A	NP_001311249.1
	MAST2	NM_001319245.2		c.177+3922G>A		intron	N/A	NP_001306174.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAST2	ENST00000361297.7	TSL:1 MANE Select	c.177+3922G>A		intron	N/A	ENSP00000354671.2
	MAST2	ENST00000470809.1	TSL:3	n.147-16439G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51600 AN: 151974 Hom.: 9159 Cov.: 32

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.340 AC: 51674 AN: 152090 Hom.: 9185 Cov.: 32 AF XY: 0.338 AC XY: 25168 AN XY: 74362

African (AFR) AF: 0.436 AC: 18068 AN: 41478

American (AMR) AF: 0.339 AC: 5175 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1078 AN: 3466

East Asian (EAS) AF: 0.326 AC: 1689 AN: 5176

South Asian (SAS) AF: 0.389 AC: 1881 AN: 4830

European-Finnish (FIN) AF: 0.261 AC: 2761 AN: 10580

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19899 AN: 67970

Other (OTH) AF: 0.347 AC: 733 AN: 2112

Alfa AF: 0.318 Hom.: 3642

Bravo AF: 0.347

Asia WGS AF: 0.354 AC: 1231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.3
DANN	Benign	0.55
PhyloP100		-0.29
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: rs10437063; hg19: chr1-46273666;