rs10763642

Variant names:

• chr10-28099221-G-A
• rs10763642
• NM_001318170.2:c.953-9380C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.923

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MPP7	NM_001318170.2	c.953-9380C>T		intron_variant	Intron 11 of 16	ENST00000683449.1	NP_001305099.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MPP7	ENST00000683449.1	c.953-9380C>T		intron_variant	Intron 11 of 16		NM_001318170.2	ENSP00000507917.1

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37230 AN: 151740 Hom.: 6307 Cov.: 32

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.: 32 AF XY: 0.255 AC XY: 18947 AN XY: 74200

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.765

Gnomad4 SAS AF: 0.394

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.246

Alfa AF: 0.153 Hom.: 5032

Bravo AF: 0.262

Asia WGS AF: 0.595 AC: 2065 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.17
DANN	Benign	0.74

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

LitVar

Other links and lift over

dbSNP: rs10763642; hg19: chr10-28388150;