rs1697137

Positions:

• chr5-67156347-G-A

Variant summary

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

The NM_001164664.2(MAST4):​c.3648+2767G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 152,070 control chromosomes in the GnomAD database, including 21,971 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 0.50 (21971 hom., cov: 32)
• Consequence: MAST4 NM_001164664.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.529

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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAST4	NM_001164664.2	c.3648+2767G>A		intron_variant		ENST00000403625.7	NP_001158136.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAST4	ENST00000403625.7	c.3648+2767G>A		intron_variant		5	NM_001164664.2	ENSP00000385727.1

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75320 AN: 151952 Hom.: 21962 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.495 AC: 75330 AN: 152070 Hom.: 21971 Cov.: 32 AF XY: 0.494 AC XY: 36738 AN XY: 74304

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.519

Gnomad4 ASJ AF: 0.532

Gnomad4 EAS AF: 0.636

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.601

Gnomad4 NFE AF: 0.651

Gnomad4 OTH AF: 0.497

Alfa AF: 0.621 Hom.: 47339

Bravo AF: 0.476

Asia WGS AF: 0.542 AC: 1888 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
DANN	Benign	0.72

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: rs1697137; hg19: chr5-66452175;