rs660745

Variant names:

• chr19-48716202-T-C
• rs660745
• NM_001130915.2:c.98-435A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 16 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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001130915.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAMSTR	NM_001130915.2	MANE Select	c.98-435A>G		intron	N/A	NP_001124387.1	Q6ZN01-1
	MAMSTR	NM_182574.3		c.-362-285A>G		intron	N/A	NP_872380.1	Q6ZN01-2
	MAMSTR	NM_001297753.2		c.-362-285A>G		intron	N/A	NP_001284682.1	Q6ZN01-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAMSTR	ENST00000318083.11	TSL:2 MANE Select	c.98-435A>G		intron	N/A	ENSP00000324175.5	Q6ZN01-1
	MAMSTR	ENST00000594582.1	TSL:1	c.-362-285A>G		intron	N/A	ENSP00000471590.1	Q6ZN01-3
	MAMSTR	ENST00000599703.2	TSL:5	c.98-285A>G		intron	N/A	ENSP00000469544.2	M0QY28

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

African (AFR) AF: 0.477 AC: 19643 AN: 41170

American (AMR) AF: 0.388 AC: 5883 AN: 15168

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1742 AN: 3464

East Asian (EAS) AF: 0.0207 AC: 106 AN: 5126

South Asian (SAS) AF: 0.261 AC: 1249 AN: 4780

European-Finnish (FIN) AF: 0.419 AC: 4374 AN: 10450

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.518 AC: 35107 AN: 67770

Other (OTH) AF: 0.471 AC: 989 AN: 2098

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.58
PhyloP100		-0.40
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs660745; hg19: chr19-49219459;