dbSNP rs10763642: MPP7:c.953-9380C>T (chr10-28099221-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001318170.2(MPP7):c.953-9380C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 151,858 control chromosomes in the GnomAD database, including 6,319 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 0.25 ( 6319 hom., cov: 32)

Consequence

MPP7
NM_001318170.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.923

Publications

10 publications found

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]

MPP7 links:

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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=-0.96).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001318170.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MPP7	NM_001318170.2	MANE Select	c.953-9380C>T	intron	N/A	NP_001305099.1	Q5T2T1-1
MPP7	NM_173496.5		c.953-9380C>T	intron	N/A	NP_775767.2	Q5T2T1-1
MPP7	NR_134517.2		n.1288-9380C>T	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MPP7	ENST00000683449.1	MANE Select	c.953-9380C>T	intron	N/A	ENSP00000507917.1	Q5T2T1-1
MPP7	ENST00000375719.7	TSL:1	c.953-9380C>T	intron	N/A	ENSP00000364871.3	Q5T2T1-1
MPP7	ENST00000496637.6	TSL:1	n.953-9380C>T	intron	N/A	ENSP00000473899.1	S4R337

Frequencies

GnomAD3 genomes

AF:

0.245

AC:

37230

AN:

151740

Hom.:

6307

Cov.:

show subpopulations

Gnomad AFR

AF:

0.353

Gnomad AMI

AF:

0.0419

Gnomad AMR

AF:

0.317

Gnomad ASJ

AF:

0.114

Gnomad EAS

AF:

0.765

Gnomad SAS

AF:

0.394

Gnomad FIN

AF:

0.234

Gnomad MID

AF:

0.165

Gnomad NFE

AF:

0.125

Gnomad OTH

AF:

0.242

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

GnomAD4 genome

AF:

0.245

AC:

37278

AN:

151858

Hom.:

6319

Cov.:

AF XY:

0.255

AC XY:

18947

AN XY:

74200

show subpopulations

African (AFR)

AF:

0.353

AC:

14621

AN:

41402

American (AMR)

AF:

0.318

AC:

4859

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.114

AC:

394

AN:

3464

East Asian (EAS)

AF:

0.765

AC:

3945

AN:

5158

South Asian (SAS)

AF:

0.394

AC:

1896

AN:

4814

European-Finnish (FIN)

AF:

0.234

AC:

2461

AN:

10496

Middle Eastern (MID)

AF:

0.156

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.125

AC:

8499

AN:

67934

Other (OTH)

AF:

0.246

AC:

519

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1235

2470

3705

4940

6175

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

380

760

1140

1520

1900

<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:

0.170

Hom.:

9609

Bravo

AF:

0.262

Asia WGS

AF:

0.595

AC:

2065

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.17

(source)

DANN

Benign

0.74

PhyloP100

-0.92

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over