chr10-28175824-G-A

Variant names:

• chr10-28175824-G-A
• rs7068246
• NM_001318170.2:c.157-25765C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_173496.5(MPP7):​c.157-25765C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 151,884 control chromosomes in the GnomAD database, including 7,816 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 0.29 (7816 hom., cov: 31)
• Consequence: MPP7 NM_173496.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.181
• Publications: 3 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173496.5. 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
	MPP7	NM_001318170.2	MANE Select	c.157-25765C>T		intron	N/A	NP_001305099.1
	MPP7	NM_173496.5		c.157-25765C>T		intron	N/A	NP_775767.2
	MPP7	NR_134517.2		n.492-25765C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MPP7	ENST00000683449.1	MANE Select	c.157-25765C>T		intron	N/A	ENSP00000507917.1
	MPP7	ENST00000375719.7	TSL:1	c.157-25765C>T		intron	N/A	ENSP00000364871.3
	MPP7	ENST00000496637.6	TSL:1	n.157-25765C>T		intron	N/A	ENSP00000473899.1

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44448 AN: 151766 Hom.: 7794 Cov.: 31

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.293 AC: 44510 AN: 151884 Hom.: 7816 Cov.: 31 AF XY: 0.292 AC XY: 21664 AN XY: 74224

African (AFR) AF: 0.461 AC: 19082 AN: 41418

American (AMR) AF: 0.353 AC: 5387 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 452 AN: 3470

East Asian (EAS) AF: 0.484 AC: 2486 AN: 5134

South Asian (SAS) AF: 0.224 AC: 1079 AN: 4814

European-Finnish (FIN) AF: 0.207 AC: 2183 AN: 10548

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.192 AC: 13026 AN: 67928

Other (OTH) AF: 0.276 AC: 582 AN: 2108

Alfa AF: 0.191 Hom.: 1627

Bravo AF: 0.315

Asia WGS AF: 0.350 AC: 1218 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.42
PhyloP100		-0.18
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7068246; hg19: chr10-28464753;