rs273504

Positions:

• chr19-18104437-A-G

Variant summary

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

The NM_001393504.1(MAST3):​c.40-3150A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.458 in 151,330 control chromosomes in the GnomAD database, including 16,279 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 0.46 (16279 hom., cov: 28)
• Consequence: MAST3 NM_001393504.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.450

Genes affected

MAST3 (HGNC:19036): (microtubule associated serine/threonine kinase 3) Predicted to enable protein serine/threonine kinase activity. Predicted to be involved in cytoskeleton organization; intracellular signal transduction; and peptidyl-serine phosphorylation. [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 = 0.534 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAST3	NM_001393504.1	c.40-3150A>G		intron_variant		ENST00000687212.1	NP_001380433.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAST3	ENST00000687212.1	c.40-3150A>G		intron_variant			NM_001393504.1	ENSP00000509890	A2
MAST3	ENST00000262811.10	c.40-3150A>G		intron_variant		1		ENSP00000262811	P2
MAST3	ENST00000697700.2	c.40-3150A>G		intron_variant				ENSP00000513407
MAST3	ENST00000704363.1	c.40-3150A>G		intron_variant				ENSP00000515871

Frequencies

GnomAD3 genomes AF: 0.458 AC: 69221 AN: 151212 Hom.: 16246 Cov.: 28

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.458 AC: 69313 AN: 151330 Hom.: 16279 Cov.: 28 AF XY: 0.459 AC XY: 33901 AN XY: 73894

Gnomad4 AFR AF: 0.540

Gnomad4 AMR AF: 0.465

Gnomad4 ASJ AF: 0.432

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.491

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.468

Alfa AF: 0.446 Hom.: 14771

Bravo AF: 0.466

Asia WGS AF: 0.333 AC: 1162 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	4.5
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: rs273504; hg19: chr19-18215247;