rs1317790

Variant names:

• chr10-28090675-G-A
• rs1317790
• NM_001318170.2:c.953-834C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-28090675-G-A
• chr10-28090675-G-C
• chr10-28090675-G-T

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 7 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.487 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MPP7	NM_001318170.2	MANE Select	c.953-834C>T		intron	N/A	NP_001305099.1
	MPP7	NM_173496.5		c.953-834C>T		intron	N/A	NP_775767.2
	MPP7	NR_134517.2		n.1288-834C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MPP7	ENST00000683449.1	MANE Select	c.953-834C>T		intron	N/A	ENSP00000507917.1
	MPP7	ENST00000375719.7	TSL:1	c.953-834C>T		intron	N/A	ENSP00000364871.3
	MPP7	ENST00000496637.6	TSL:1	n.953-834C>T		intron	N/A	ENSP00000473899.1

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18232 AN: 152048 Hom.: 1725 Cov.: 32

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

African (AFR) AF: 0.0920 AC: 3821 AN: 41530

American (AMR) AF: 0.201 AC: 3072 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0597 AC: 207 AN: 3466

East Asian (EAS) AF: 0.503 AC: 2604 AN: 5172

South Asian (SAS) AF: 0.274 AC: 1322 AN: 4818

European-Finnish (FIN) AF: 0.161 AC: 1706 AN: 10576

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0765 AC: 5204 AN: 68010

Other (OTH) AF: 0.134 AC: 283 AN: 2114

Alfa AF: 0.0914 Hom.: 4137

Bravo AF: 0.125

Asia WGS AF: 0.416 AC: 1447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.37
DANN	Benign	0.71
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1317790; hg19: chr10-28379604;