rs194469

Variant names:

• chr5-66890713-G-A
• rs194469
• NM_001164664.2:c.643-9238G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-66890713-G-A
• chr5-66890713-G-C

Variant summary

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

The NM_001164664.2(MAST4):​c.643-9238G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 151,890 control chromosomes in the GnomAD database, including 16,813 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 0.47 (16813 hom., cov: 31)
• Consequence: MAST4 NM_001164664.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162
• Publications: 2 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.656 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.643-9238G>A		intron	N/A	NP_001158136.1	O15021-5
	MAST4	NM_001393524.1		c.643-9238G>A		intron	N/A	NP_001380453.1
	MAST4	NM_001393525.1		c.643-9238G>A		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.643-9238G>A		intron	N/A	ENSP00000385727.1	O15021-5
	MAST4	ENST00000403666.5	TSL:1	c.40-9238G>A		intron	N/A	ENSP00000384313.1	O15021-3
	MAST4	ENST00000406374.5	TSL:1	c.643-9238G>A		intron	N/A	ENSP00000385088.1	O15021-4

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70625 AN: 151772 Hom.: 16785 Cov.: 31

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.465 AC: 70692 AN: 151890 Hom.: 16813 Cov.: 31 AF XY: 0.474 AC XY: 35175 AN XY: 74194

African (AFR) AF: 0.404 AC: 16709 AN: 41408

American (AMR) AF: 0.498 AC: 7596 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1756 AN: 3464

East Asian (EAS) AF: 0.674 AC: 3466 AN: 5140

South Asian (SAS) AF: 0.549 AC: 2644 AN: 4816

European-Finnish (FIN) AF: 0.563 AC: 5932 AN: 10532

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.458 AC: 31108 AN: 67966

Other (OTH) AF: 0.462 AC: 975 AN: 2110

Alfa AF: 0.461 Hom.: 2081

Bravo AF: 0.456

Asia WGS AF: 0.586 AC: 2038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.5
DANN	Benign	0.61
PhyloP100		-0.16
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: rs194469; hg19: chr5-66186541;