rs10437063

chr1-45807994-G-A

Variant summary

Our verdict is Benign. Variant got -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

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 (AFR) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAST2	NM_015112.3	c.177+3922G>A		intron_variant		ENST00000361297.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAST2	ENST00000361297.7	c.177+3922G>A		intron_variant		1	NM_015112.3
MAST2	ENST00000470809.1	n.147-16439G>A		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.436

Gnomad4 AMR AF: 0.339

Gnomad4 ASJ AF: 0.311

Gnomad4 EAS AF: 0.326

Gnomad4 SAS AF: 0.389

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.347

Alfa AF: 0.314 Hom.: 2990

Bravo AF: 0.347

Asia WGS AF: 0.354 AC: 1231 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	4.3
Dann	Benign	0.55

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: rs10437063; hg19: chr1-46273666;