rs9687339

chr5-66672344-C-A

Variant summary

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

The NM_001164664.2(MAST4):c.363+75326C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 151,980 control chromosomes in the GnomAD database, including 7,741 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 0.31 (7741 hom., cov: 32)
• Consequence: MAST4 NM_001164664.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAST4	NM_001164664.2	c.363+75326C>A		intron_variant		ENST00000403625.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAST4	ENST00000403625.7	c.363+75326C>A		intron_variant		5	NM_001164664.2	A2
MAST4	ENST00000406039.5	c.363+75326C>A		intron_variant		1
MAST4	ENST00000406374.5	c.363+75326C>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47298 AN: 151862 Hom.: 7731 Cov.: 32

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.312 AC: 47343 AN: 151980 Hom.: 7741 Cov.: 32 AF XY: 0.308 AC XY: 22872 AN XY: 74302

Gnomad4 AFR AF: 0.403

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.287

Gnomad4 OTH AF: 0.276

Alfa AF: 0.286 Hom.: 8455

Bravo AF: 0.309

Asia WGS AF: 0.319 AC: 1108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.30
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9687339; hg19: chr5-65968172;