rs676388

Positions:

• chr19-48708712-T-C

Variant summary

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

The XM_047438640.1(MAMSTR):​c.601-1301A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 151,950 control chromosomes in the GnomAD database, including 17,364 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 0.46 (17364 hom., cov: 32)
• Consequence: MAMSTR XM_047438640.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86

Genes affected

MAMSTR (HGNC:26689): (MEF2 activating motif and SAP domain containing transcriptional regulator) Predicted to enable transcription coregulator activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within positive regulation of myotube differentiation and positive regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.517 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAMSTR	XM_047438640.1	c.601-1301A>G		intron_variant			XP_047294596.1
		n.48708712T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70475 AN: 151832 Hom.: 17348 Cov.: 32

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.00385

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.464 AC: 70526 AN: 151950 Hom.: 17364 Cov.: 32 AF XY: 0.451 AC XY: 33523 AN XY: 74266

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.387

Gnomad4 ASJ AF: 0.475

Gnomad4 EAS AF: 0.00386

Gnomad4 SAS AF: 0.284

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.478

Alfa AF: 0.473 Hom.: 9390

Bravo AF: 0.467

Asia WGS AF: 0.150 AC: 529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.0
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs676388; hg19: chr19-49211969;