1-45869204-A-G

Variant names:

• chr1-45869204-A-G
• rs4660318
• NM_015112.3:c.469-13160A>G

Variant summary

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

The NM_015112.3(MAST2):​c.469-13160A>G 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 151,894 control chromosomes in the GnomAD database, including 9,181 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 (9181 hom., cov: 32)
• Consequence: MAST2 NM_015112.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.565
• Publications: 8 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]

LOC105378694 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAST2	NM_015112.3	c.469-13160A>G		intron_variant	Intron 3 of 28	ENST00000361297.7	NP_055927.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAST2	ENST00000361297.7	c.469-13160A>G		intron_variant	Intron 3 of 28	1	NM_015112.3	ENSP00000354671.2
MAST2	ENST00000470809.1	n.438-13160A>G		intron_variant	Intron 3 of 4	3

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51575 AN: 151776 Hom.: 9154 Cov.: 32

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.262

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: 51651 AN: 151894 Hom.: 9181 Cov.: 32 AF XY: 0.339 AC XY: 25151 AN XY: 74216

African (AFR) AF: 0.436 AC: 18072 AN: 41420

American (AMR) AF: 0.339 AC: 5162 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1081 AN: 3470

East Asian (EAS) AF: 0.327 AC: 1687 AN: 5158

South Asian (SAS) AF: 0.389 AC: 1875 AN: 4816

European-Finnish (FIN) AF: 0.262 AC: 2766 AN: 10546

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

European-Non Finnish (NFE) AF: 0.293 AC: 19890 AN: 67928

Other (OTH) AF: 0.348 AC: 733 AN: 2108

Alfa AF: 0.308 Hom.: 3926

Bravo AF: 0.347

Asia WGS AF: 0.354 AC: 1232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	10
DANN	Benign	0.87
PhyloP100		0.56
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: rs4660318; hg19: chr1-46334876;