rs9687339

Variant names:

• chr5-66672344-C-A
• rs9687339
• NM_001164664.2:c.363+75326C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001164664.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAST4	NM_001164664.2	MANE Select	c.363+75326C>A		intron	N/A	NP_001158136.1
	MAST4	NM_001393524.1		c.363+75326C>A		intron	N/A	NP_001380453.1
	MAST4	NM_001393525.1		c.363+75326C>A		intron	N/A	NP_001380454.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAST4	ENST00000403625.7	TSL:5 MANE Select	c.363+75326C>A		intron	N/A	ENSP00000385727.1
	MAST4	ENST00000406374.5	TSL:1	c.363+75326C>A		intron	N/A	ENSP00000385088.1
	MAST4	ENST00000406039.5	TSL:1	c.363+75326C>A		intron	N/A	ENSP00000384547.1

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

African (AFR) AF: 0.403 AC: 16693 AN: 41418

American (AMR) AF: 0.215 AC: 3281 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 879 AN: 3466

East Asian (EAS) AF: 0.299 AC: 1550 AN: 5182

South Asian (SAS) AF: 0.329 AC: 1583 AN: 4818

European-Finnish (FIN) AF: 0.282 AC: 2977 AN: 10558

Middle Eastern (MID) AF: 0.260 AC: 76 AN: 292

European-Non Finnish (NFE) AF: 0.287 AC: 19488 AN: 67950

Other (OTH) AF: 0.276 AC: 583 AN: 2110

Alfa AF: 0.287 Hom.: 10886

Bravo AF: 0.309

Asia WGS AF: 0.319 AC: 1108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.30
DANN	Benign	0.46
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs9687339; hg19: chr5-65968172;