chr1-45917911-C-G

Variant names:

• chr1-45917911-C-G
• rs10789481
• NM_015112.3:c.500+35516C>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.500+35516C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 151,942 control chromosomes in the GnomAD database, including 15,610 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 0.45 (15610 hom., cov: 31)
• Consequence: MAST2 NM_015112.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581
• Publications: 7 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAST2	NM_015112.3	c.500+35516C>G		intron_variant	Intron 4 of 28	ENST00000361297.7	NP_055927.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAST2	ENST00000361297.7	c.500+35516C>G		intron_variant	Intron 4 of 28	1	NM_015112.3	ENSP00000354671.2
MAST2	ENST00000674079.1	c.50+4032C>G		intron_variant	Intron 1 of 26			ENSP00000501318.1
MAST2	ENST00000372008.6	c.155+378C>G		intron_variant	Intron 2 of 19	5		ENSP00000361078.2

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68486 AN: 151824 Hom.: 15625 Cov.: 31

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.451 AC: 68465 AN: 151942 Hom.: 15610 Cov.: 31 AF XY: 0.451 AC XY: 33496 AN XY: 74268

African (AFR) AF: 0.424 AC: 17551 AN: 41438

American (AMR) AF: 0.493 AC: 7534 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1634 AN: 3468

East Asian (EAS) AF: 0.625 AC: 3227 AN: 5166

South Asian (SAS) AF: 0.447 AC: 2148 AN: 4802

European-Finnish (FIN) AF: 0.414 AC: 4368 AN: 10552

Middle Eastern (MID) AF: 0.394 AC: 115 AN: 292

European-Non Finnish (NFE) AF: 0.449 AC: 30506 AN: 67944

Other (OTH) AF: 0.441 AC: 930 AN: 2108

Alfa AF: 0.446 Hom.: 1888

Bravo AF: 0.456

Asia WGS AF: 0.523 AC: 1815 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.9
DANN	Benign	0.55
PhyloP100		-0.58
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: rs10789481; hg19: chr1-46383583; COSMIC: COSV63617010; COSMIC: COSV63617010;