rs1364020

Positions:

• chr5-66793009-A-G

Variant summary

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

The NM_001164664.2(MAST4):​c.642+4215A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0489 in 152,290 control chromosomes in the GnomAD database, including 274 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 0.049 (274 hom., cov: 33)
• Consequence: MAST4 NM_001164664.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.406

Genes affected

MAST4 (HGNC:19037): (microtubule associated serine/threonine kinase family member 4) This gene encodes a member of the microtubule-associated serine/threonine protein kinases. The proteins in this family contain a domain that gives the kinase the ability to determine its own scaffold to control the effects of their kinase activities. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Mar 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAST4	NM_001164664.2	c.642+4215A>G		intron_variant		ENST00000403625.7	NP_001158136.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAST4	ENST00000403625.7	c.642+4215A>G		intron_variant		5	NM_001164664.2	ENSP00000385727	A2

Frequencies

GnomAD3 genomes AF: 0.0488 AC: 7433 AN: 152174 Hom.: 273 Cov.: 33

Gnomad AFR AF: 0.0856

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0491

Gnomad ASJ AF: 0.0764

Gnomad EAS AF: 0.0800

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.0216

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0215

Gnomad OTH AF: 0.0422

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

GnomAD4 genome AF: 0.0489 AC: 7448 AN: 152290 Hom.: 274 Cov.: 33 AF XY: 0.0507 AC XY: 3776 AN XY: 74476

Gnomad4 AFR AF: 0.0856

Gnomad4 AMR AF: 0.0491

Gnomad4 ASJ AF: 0.0764

Gnomad4 EAS AF: 0.0800

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.0216

Gnomad4 NFE AF: 0.0215

Gnomad4 OTH AF: 0.0465

Alfa AF: 0.0358 Hom.: 25

Bravo AF: 0.0509

Asia WGS AF: 0.123 AC: 427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	4.1
DANN	Benign	0.74

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1364020; hg19: chr5-66088837;