rs7094791

Variant names:

• chr10-46035886-A-G
• rs7094791
• NM_002443.4:c.216-2335T>C

Variant summary

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

The NM_002443.4(MSMB):​c.216-2335T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 152,070 control chromosomes in the GnomAD database, including 15,578 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 0.42 (15578 hom., cov: 32)
• Consequence: MSMB NM_002443.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• Publications: 8 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]

ENSG00000305167 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002443.4. 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
	MSMB	NM_002443.4	MANE Select	c.216-2335T>C		intron	N/A	NP_002434.1
	MSMB	NM_138634.3		c.110-2335T>C		intron	N/A	NP_619540.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MSMB	ENST00000582163.3	TSL:1 MANE Select	c.216-2335T>C		intron	N/A	ENSP00000463092.1
	MSMB	ENST00000581478.5	TSL:1	c.110-2335T>C		intron	N/A	ENSP00000462641.1
	MSMB	ENST00000663171.1		c.216-2318T>C		intron	N/A	ENSP00000499419.1

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64403 AN: 151952 Hom.: 15546 Cov.: 32

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.424 AC: 64473 AN: 152070 Hom.: 15578 Cov.: 32 AF XY: 0.419 AC XY: 31146 AN XY: 74342

African (AFR) AF: 0.678 AC: 28120 AN: 41460

American (AMR) AF: 0.337 AC: 5145 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1308 AN: 3462

East Asian (EAS) AF: 0.316 AC: 1638 AN: 5176

South Asian (SAS) AF: 0.340 AC: 1638 AN: 4824

European-Finnish (FIN) AF: 0.298 AC: 3146 AN: 10564

Middle Eastern (MID) AF: 0.346 AC: 101 AN: 292

European-Non Finnish (NFE) AF: 0.327 AC: 22266 AN: 67994

Other (OTH) AF: 0.397 AC: 834 AN: 2102

Alfa AF: 0.352 Hom.: 7880

Bravo AF: 0.437

Asia WGS AF: 0.359 AC: 1250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.28
DANN	Benign	0.41
PhyloP100		-1.4

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: rs7094791; hg19: chr10-51559936;