GeneBe

19-48711213-T-C

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.777

Publications

35 publications found
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]

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank MANE Protein UniProt
MAMSTRXM_047438640.1 linkc.600+2647A>G 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:
0.396
AC:
60263
AN:
151992
Hom.:
12742
Cov.:
33
show subpopulations
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
show subpopulations
African (AFR)
AF:
0.323
AC:
13410
AN:
41486
American (AMR)
AF:
0.462
AC:
7061
AN:
15280
Ashkenazi Jewish (ASJ)
AF:
0.448
AC:
1553
AN:
3466
East Asian (EAS)
AF:
0.847
AC:
4380
AN:
5174
South Asian (SAS)
AF:
0.430
AC:
2072
AN:
4814
European-Finnish (FIN)
AF:
0.449
AC:
4757
AN:
10586
Middle Eastern (MID)
AF:
0.303
AC:
89
AN:
294
European-Non Finnish (NFE)
AF:
0.379
AC:
25785
AN:
67986
Other (OTH)
AF:
0.396
AC:
838
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
1827
3654
5482
7309
9136
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
590
1180
1770
2360
2950
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.394
Hom.:
43925
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
PhyloP100
-0.78

Splicing

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

Publications

Other links and lift over

dbSNP: rs281380; hg19: chr19-49214470; API