10-46046326-A-A

Variant names:

• chr10-46046326-A-A
• ENST00000663171.1:c.

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The ENST00000663171.1(MSMB):​c. variant causes a exon region change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as risk factor (no stars).

• Frequency: Genomes: not found (cov: 33)
• Consequence: MSMB ENST00000663171.1 exon_region
• Clinical Significance: risk factor no assertion criteria provided O:1
• Conservation: PhyloP100: 0.102
• Publications: 0 publications found

Genes affected

MSMB (HGNC:7372): (microseminoprotein beta) The protein encoded by this gene is a member of the immunoglobulin binding factor family. It is synthesized by the epithelial cells of the prostate gland and secreted into the seminal plasma. This protein has inhibin-like activity. It may have a role as an autocrine paracrine factor in uterine, breast and other female reproductive tissues. The expression of the encoded protein is found to be decreased in prostate cancer. Two alternatively spliced transcript variants encoding different isoforms are described for this gene. The use of alternate polyadenylation sites has been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MSMB	NM_002443.4	c.		upstream_gene_variant		ENST00000582163.3	NP_002434.1
MSMB	NM_138634.3	c.		upstream_gene_variant			NP_619540.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MSMB	ENST00000663171.1	c.		exon_region	Exon 2 of 5			ENSP00000499419.1
MSMB	ENST00000663171.1	c.		5_prime_UTR_variant	Exon 2 of 5			ENSP00000499419.1
MSMB	ENST00000582163.3	c.		upstream_gene_variant		1	NM_002443.4	ENSP00000463092.1
MSMB	ENST00000581478.5	c.		upstream_gene_variant		1		ENSP00000462641.1

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Significance: risk factor

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Prostate cancer, hereditary, 13 Other:1

Oct 18, 2018

OMIM

Significance: risk factor

Review Status: no assertion criteria provided

Collection Method: literature only

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.10

Splicing

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

Other links and lift over

hg19: chr10-51549496;