rs281379

Variant names:

• chr19-48711017-G-A
• rs281379
• XM_047438640.1:c.600+2843C>T

Variant summary

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

The XM_047438640.1(MAMSTR):​c.600+2843C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 152,018 control chromosomes in the GnomAD database, including 12,250 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 0.38 (12250 hom., cov: 32)
• Consequence: MAMSTR XM_047438640.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.411
• Publications: 77 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAMSTR	XM_047438640.1	c.600+2843C>T		intron_variant	Intron 6 of 6		XP_047294596.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57336 AN: 151900 Hom.: 12251 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.00346

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.377 AC: 57356 AN: 152018 Hom.: 12250 Cov.: 32 AF XY: 0.368 AC XY: 27350 AN XY: 74306

African (AFR) AF: 0.241 AC: 9969 AN: 41436

American (AMR) AF: 0.348 AC: 5307 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1659 AN: 3468

East Asian (EAS) AF: 0.00347 AC: 18 AN: 5192

South Asian (SAS) AF: 0.265 AC: 1279 AN: 4820

European-Finnish (FIN) AF: 0.404 AC: 4269 AN: 10558

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.493 AC: 33498 AN: 67978

Other (OTH) AF: 0.411 AC: 867 AN: 2110

Alfa AF: 0.439 Hom.: 51098

Bravo AF: 0.368

Asia WGS AF: 0.139 AC: 489 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.87
DANN	Benign	0.58
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs281379; hg19: chr19-49214274;