rs10500564

chr5-66950182-G-Achr5-66950182-G-T

Variant summary

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

The NM_001164664.2(MAST4):c.674+50200G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0553 in 151,790 control chromosomes in the GnomAD database, including 333 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 0.055 (333 hom., cov: 32)
• Consequence: MAST4 NM_001164664.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.084 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAST4	NM_001164664.2	c.674+50200G>A		intron_variant		ENST00000403625.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAST4	ENST00000403625.7	c.674+50200G>A		intron_variant		5	NM_001164664.2	A2

Frequencies

GnomAD3 genomes AF: 0.0553 AC: 8389 AN: 151672 Hom.: 332 Cov.: 32

Gnomad AFR AF: 0.0160

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.0651

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.000580

Gnomad SAS AF: 0.0913

Gnomad FIN AF: 0.0621

Gnomad MID AF: 0.0987

Gnomad NFE AF: 0.0726

Gnomad OTH AF: 0.0635

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

GnomAD4 genome AF: 0.0553 AC: 8388 AN: 151790 Hom.: 333 Cov.: 32 AF XY: 0.0566 AC XY: 4198 AN XY: 74180

Gnomad4 AFR AF: 0.0160

Gnomad4 AMR AF: 0.0651

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.000581

Gnomad4 SAS AF: 0.0910

Gnomad4 FIN AF: 0.0621

Gnomad4 NFE AF: 0.0726

Gnomad4 OTH AF: 0.0629

Alfa AF: 0.0651 Hom.: 111

Bravo AF: 0.0531

Asia WGS AF: 0.0320 AC: 111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.43
Dann	Benign	0.41

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: rs10500564; hg19: chr5-66246010;