rs10669586

chr10-46046598-C-CAG

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000663171.1(MSMB):c.-142-220_-142-219insCT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.916 in 152,072 control chromosomes in the GnomAD database, including 64,507 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.92 (64507 hom., cov: 0)
• Consequence: MSMB ENST00000663171.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51

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

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.978 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MSMB	ENST00000663171.1	c.-142-220_-142-219insCT		intron_variant

Frequencies

GnomAD3 genomes AF: 0.916 AC: 139187 AN: 151954 Hom.: 64484 Cov.: 0

Gnomad AFR AF: 0.754

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.961

Gnomad ASJ AF: 0.961

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.943

Gnomad FIN AF: 0.968

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.984

Gnomad OTH AF: 0.934

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

GnomAD4 genome AF: 0.916 AC: 139260 AN: 152072 Hom.: 64507 Cov.: 0 AF XY: 0.918 AC XY: 68226 AN XY: 74358

Gnomad4 AFR AF: 0.753

Gnomad4 AMR AF: 0.961

Gnomad4 ASJ AF: 0.961

Gnomad4 EAS AF: 0.995

Gnomad4 SAS AF: 0.943

Gnomad4 FIN AF: 0.968

Gnomad4 NFE AF: 0.984

Gnomad4 OTH AF: 0.934

Alfa AF: 0.943 Hom.: 8303

Bravo AF: 0.905

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10669586; hg19: chr10-51549224;