rs1317790

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001318170.2(MPP7):​c.953-834C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,166 control chromosomes in the GnomAD database, including 1,737 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 0.12 ( 1737 hom., cov: 32)

Consequence

MPP7
NM_001318170.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.10
Variant links:
Genes affected
MPP7 (HGNC:26542): (MAGUK p55 scaffold protein 7) The protein encoded by this gene is a member of the p55 Stardust family of membrane-associated guanylate kinase (MAGUK) proteins, which function in the establishment of epithelial cell polarity. This family member forms a complex with the polarity protein DLG1 (discs, large homolog 1) and facilitates epithelial cell polarity and tight junction formation. Polymorphisms in this gene are associated with variations in site-specific bone mineral density (BMD). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MPP7NM_001318170.2 linkuse as main transcriptc.953-834C>T intron_variant ENST00000683449.1 NP_001305099.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MPP7ENST00000683449.1 linkuse as main transcriptc.953-834C>T intron_variant NM_001318170.2 ENSP00000507917 P1Q5T2T1-1

Frequencies

GnomAD3 genomes
AF:
0.120
AC:
18232
AN:
152048
Hom.:
1725
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0921
Gnomad AMI
AF:
0.0330
Gnomad AMR
AF:
0.200
Gnomad ASJ
AF:
0.0597
Gnomad EAS
AF:
0.503
Gnomad SAS
AF:
0.274
Gnomad FIN
AF:
0.161
Gnomad MID
AF:
0.0538
Gnomad NFE
AF:
0.0765
Gnomad OTH
AF:
0.129
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.120
AC:
18264
AN:
152166
Hom.:
1737
Cov.:
32
AF XY:
0.129
AC XY:
9630
AN XY:
74384
show subpopulations
Gnomad4 AFR
AF:
0.0920
Gnomad4 AMR
AF:
0.201
Gnomad4 ASJ
AF:
0.0597
Gnomad4 EAS
AF:
0.503
Gnomad4 SAS
AF:
0.274
Gnomad4 FIN
AF:
0.161
Gnomad4 NFE
AF:
0.0765
Gnomad4 OTH
AF:
0.134
Alfa
AF:
0.0858
Hom.:
1656
Bravo
AF:
0.125
Asia WGS
AF:
0.416
AC:
1447
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.37
DANN
Benign
0.71

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

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

Other links and lift over

dbSNP: rs1317790; hg19: chr10-28379604; API