19-48711213-T-C

Position:

• chr19-48711213-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.600+2647A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 152,110 control chromosomes in the GnomAD database, including 12,753 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 0.40 (12753 hom., cov: 33)
• Consequence: MAMSTR XM_047438640.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.777

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.826 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAMSTR	XM_047438640.1	c.600+2647A>G		intron_variant			XP_047294596.1
		n.48711213T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60263 AN: 151992 Hom.: 12742 Cov.: 33

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.847

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.397 AC: 60324 AN: 152110 Hom.: 12753 Cov.: 33 AF XY: 0.403 AC XY: 29998 AN XY: 74374

Gnomad4 AFR AF: 0.323

Gnomad4 AMR AF: 0.462

Gnomad4 ASJ AF: 0.448

Gnomad4 EAS AF: 0.847

Gnomad4 SAS AF: 0.430

Gnomad4 FIN AF: 0.449

Gnomad4 NFE AF: 0.379

Gnomad4 OTH AF: 0.396

Alfa AF: 0.392 Hom.: 18091

Bravo AF: 0.397

Asia WGS AF: 0.642 AC: 2227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs281380; hg19: chr19-49214470;