rs660745

chr19-48716202-T-C

Variant summary

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

The NM_001130915.2(MAMSTR):c.98-435A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 151,230 control chromosomes in the GnomAD database, including 16,986 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 (16986 hom., cov: 27)
• Consequence: MAMSTR NM_001130915.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.396

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAMSTR	NM_001130915.2	c.98-435A>G		intron_variant		ENST00000318083.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAMSTR	ENST00000318083.11	c.98-435A>G		intron_variant		2	NM_001130915.2	P2

Frequencies

GnomAD3 genomes AF: 0.461 AC: 69619 AN: 151112 Hom.: 16992 Cov.: 27

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.0206

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.460 AC: 69626 AN: 151230 Hom.: 16986 Cov.: 27 AF XY: 0.450 AC XY: 33201 AN XY: 73858

Gnomad4 AFR AF: 0.477

Gnomad4 AMR AF: 0.388

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.0207

Gnomad4 SAS AF: 0.261

Gnomad4 FIN AF: 0.419

Gnomad4 NFE AF: 0.518

Gnomad4 OTH AF: 0.471

Alfa AF: 0.460 Hom.: 1829

Bravo AF: 0.459

Asia WGS AF: 0.139 AC: 490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.4
Dann	Benign	0.58

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs660745; hg19: chr19-49219459;