5-66949749-C-T

Variant names:

• chr5-66949749-C-T
• rs7714441
• NM_001164664.2:c.674+49767C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001164664.2(MAST4):​c.674+49767C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0681 in 152,004 control chromosomes in the GnomAD database, including 1,094 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 0.068 (1094 hom., cov: 32)
• Consequence: MAST4 NM_001164664.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 0 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.228 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAST4	NM_001164664.2	MANE Select	c.674+49767C>T		intron	N/A	NP_001158136.1	O15021-5
	MAST4	NM_001393524.1		c.674+49767C>T		intron	N/A	NP_001380453.1
	MAST4	NM_001393525.1		c.674+49767C>T		intron	N/A	NP_001380454.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAST4	ENST00000403625.7	TSL:5 MANE Select	c.674+49767C>T		intron	N/A	ENSP00000385727.1	O15021-5
	MAST4	ENST00000403666.5	TSL:1	c.107+32731C>T		intron	N/A	ENSP00000384313.1	O15021-3
	MAST4	ENST00000406374.5	TSL:1	c.710+32731C>T		intron	N/A	ENSP00000385088.1	O15021-4

Frequencies

GnomAD3 genomes AF: 0.0679 AC: 10317 AN: 151888 Hom.: 1087 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0284

Gnomad ASJ AF: 0.0124

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000831

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00219

Gnomad OTH AF: 0.0627

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

GnomAD4 genome AF: 0.0681 AC: 10351 AN: 152004 Hom.: 1094 Cov.: 32 AF XY: 0.0659 AC XY: 4899 AN XY: 74284

African (AFR) AF: 0.231 AC: 9583 AN: 41404

American (AMR) AF: 0.0283 AC: 432 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0124 AC: 43 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5180

South Asian (SAS) AF: 0.000624 AC: 3 AN: 4810

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10582

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.00219 AC: 149 AN: 67982

Other (OTH) AF: 0.0620 AC: 131 AN: 2112

Alfa AF: 0.0954 Hom.: 509

Bravo AF: 0.0770

Asia WGS AF: 0.0190 AC: 66 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
DANN	Benign	0.73
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7714441; hg19: chr5-66245577;