rs61847070

Positions:

• chr10-46047367-A-G

Variant summary

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

The ENST00000663171.1(MSMB):​c.-143+507T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0554 in 152,234 control chromosomes in the GnomAD database, including 270 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 0.055 (270 hom., cov: 32)
• Consequence: MSMB ENST00000663171.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0727 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MSMB	ENST00000663171.1	c.-143+507T>C		intron_variant				ENSP00000499419

Frequencies

GnomAD3 genomes AF: 0.0554 AC: 8430 AN: 152116 Hom.: 270 Cov.: 32

Gnomad AFR AF: 0.0302

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0455

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.0114

Gnomad SAS AF: 0.0790

Gnomad FIN AF: 0.0678

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0695

Gnomad OTH AF: 0.0583

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

GnomAD4 genome AF: 0.0554 AC: 8427 AN: 152234 Hom.: 270 Cov.: 32 AF XY: 0.0552 AC XY: 4109 AN XY: 74426

Gnomad4 AFR AF: 0.0301

Gnomad4 AMR AF: 0.0454

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.0114

Gnomad4 SAS AF: 0.0793

Gnomad4 FIN AF: 0.0678

Gnomad4 NFE AF: 0.0695

Gnomad4 OTH AF: 0.0577

Alfa AF: 0.0690 Hom.: 84

Bravo AF: 0.0520

Asia WGS AF: 0.0420 AC: 145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.3
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs61847070; hg19: chr10-51548455;