rs786399

Variant names:

• chr10-28316597-A-G
• rs786399
• ENST00000893162.1:c.-132+18273T>C

Your query was ambiguous. Multiple possible variants found:

• chr10-28316597-A-G
• chr10-28316597-A-T

Variant summary

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

The ENST00000893162.1(MPP7):​c.-132+18273T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 151,910 control chromosomes in the GnomAD database, including 11,580 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 0.37 (11580 hom., cov: 31)
• Consequence: MPP7 ENST00000893162.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740
• Publications: 1 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000893162.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MPP7	ENST00000893162.1		c.-132+18273T>C		intron	N/A	ENSP00000563221.1
	MPP7	ENST00000957212.1		c.-235+18273T>C		intron	N/A	ENSP00000627271.1
	MPP7	ENST00000441595.2	TSL:5	c.-132+13332T>C		intron	N/A	ENSP00000398319.1	U5GXS2

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56461 AN: 151792 Hom.: 11554 Cov.: 31

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.0703

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.372 AC: 56535 AN: 151910 Hom.: 11580 Cov.: 31 AF XY: 0.365 AC XY: 27112 AN XY: 74216

African (AFR) AF: 0.535 AC: 22163 AN: 41418

American (AMR) AF: 0.277 AC: 4225 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1223 AN: 3472

East Asian (EAS) AF: 0.0704 AC: 365 AN: 5182

South Asian (SAS) AF: 0.244 AC: 1178 AN: 4820

European-Finnish (FIN) AF: 0.337 AC: 3548 AN: 10524

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.336 AC: 22799 AN: 67950

Other (OTH) AF: 0.340 AC: 715 AN: 2100

Alfa AF: 0.343 Hom.: 39528

Bravo AF: 0.377

Asia WGS AF: 0.167 AC: 578 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.45
PhyloP100		0.074

Splicing

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

Other links and lift over

dbSNP: rs786399; hg19: chr10-28605526;