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GeneBe

19-48713926-G-A

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7

The NM_001130915.2(MAMSTR):c.843C>T(p.Ser281=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000718 in 1,612,594 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0021 ( 3 hom., cov: 33)
Exomes 𝑓: 0.00057 ( 6 hom. )

Consequence

MAMSTR
NM_001130915.2 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.09
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 19-48713926-G-A is Benign according to our data. Variant chr19-48713926-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2650218.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=1.09 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MAMSTRNM_001130915.2 linkuse as main transcriptc.843C>T p.Ser281= synonymous_variant 8/10 ENST00000318083.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MAMSTRENST00000318083.11 linkuse as main transcriptc.843C>T p.Ser281= synonymous_variant 8/102 NM_001130915.2 P2Q6ZN01-1
MAMSTRENST00000594582.1 linkuse as main transcriptc.339C>T p.Ser113= synonymous_variant 5/71 Q6ZN01-3
MAMSTRENST00000356751.8 linkuse as main transcriptc.534C>T p.Ser178= synonymous_variant 6/82 A2Q6ZN01-2

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00208
AC:
316
AN:
152210
Hom.:
1
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00634
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000785
Gnomad ASJ
AF:
0.000864
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000515
Gnomad OTH
AF:
0.00143
GnomAD3 exomes
AF:
0.000793
AC:
197
AN:
248554
Hom.:
1
AF XY:
0.000713
AC XY:
96
AN XY:
134658
show subpopulations
Gnomad AFR exome
AF:
0.00592
Gnomad AMR exome
AF:
0.000696
Gnomad ASJ exome
AF:
0.000500
Gnomad EAS exome
AF:
0.000109
Gnomad SAS exome
AF:
0.0000328
Gnomad FIN exome
AF:
0.0000467
Gnomad NFE exome
AF:
0.000439
Gnomad OTH exome
AF:
0.00329
GnomAD4 exome
AF:
0.000570
AC:
832
AN:
1460266
Hom.:
6
Cov.:
42
AF XY:
0.000562
AC XY:
408
AN XY:
726278
show subpopulations
Gnomad4 AFR exome
AF:
0.00717
Gnomad4 AMR exome
AF:
0.000761
Gnomad4 ASJ exome
AF:
0.000613
Gnomad4 EAS exome
AF:
0.000101
Gnomad4 SAS exome
AF:
0.0000464
Gnomad4 FIN exome
AF:
0.0000564
Gnomad4 NFE exome
AF:
0.000357
Gnomad4 OTH exome
AF:
0.00131
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00214
AC:
326
AN:
152328
Hom.:
3
Cov.:
33
AF XY:
0.00207
AC XY:
154
AN XY:
74490
show subpopulations
Gnomad4 AFR
AF:
0.00640
Gnomad4 AMR
AF:
0.000784
Gnomad4 ASJ
AF:
0.000864
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000515
Gnomad4 OTH
AF:
0.00473
Alfa
AF:
0.00126
Hom.:
0
Bravo
AF:
0.00229
Asia WGS
AF:
0.0130
AC:
44
AN:
3478
EpiCase
AF:
0.000545
EpiControl
AF:
0.000652

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenApr 01, 2023MAMSTR: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
Cadd
Benign
8.4
Dann
Benign
0.82

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs145040442; hg19: chr19-49217183; API