rs4660891

Positions:

• chr1-45853775-T-A
• chr1-45853775-T-C
• chr1-45853775-T-G

Variant summary

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

The NM_015112.3(MAST2):​c.468+24194T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.796 in 151,868 control chromosomes in the GnomAD database, including 48,653 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 0.80 (48653 hom., cov: 29)
• Consequence: MAST2 NM_015112.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61

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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.96 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAST2	NM_015112.3	c.468+24194T>A		intron_variant		ENST00000361297.7	NP_055927.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAST2	ENST00000361297.7	c.468+24194T>A		intron_variant		1	NM_015112.3	ENSP00000354671
MAST2	ENST00000470809.1	n.437+24194T>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.797 AC: 120886 AN: 151750 Hom.: 48621 Cov.: 29

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.982

Gnomad SAS AF: 0.842

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.788

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

GnomAD4 genome AF: 0.796 AC: 120957 AN: 151868 Hom.: 48653 Cov.: 29 AF XY: 0.796 AC XY: 59092 AN XY: 74206

Gnomad4 AFR AF: 0.882

Gnomad4 AMR AF: 0.832

Gnomad4 ASJ AF: 0.779

Gnomad4 EAS AF: 0.982

Gnomad4 SAS AF: 0.842

Gnomad4 FIN AF: 0.683

Gnomad4 NFE AF: 0.738

Gnomad4 OTH AF: 0.791

Alfa AF: 0.760 Hom.: 5176

Bravo AF: 0.809

Asia WGS AF: 0.899 AC: 3124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.6
DANN	Benign	0.56

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: rs4660891; hg19: chr1-46319447;