rs2075894

Variant names:

• chr10-46039711-A-G
• rs2075894
• NM_002443.4:c.109+275T>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.109+275T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 152,102 control chromosomes in the GnomAD database, including 6,615 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 0.26 (6615 hom., cov: 32)
• Consequence: MSMB NM_002443.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.61
• Publications: 3 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.478 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MSMB	NM_002443.4	c.109+275T>C		intron_variant	Intron 2 of 3	ENST00000582163.3	NP_002434.1
MSMB	NM_138634.3	c.109+275T>C		intron_variant	Intron 2 of 2		NP_619540.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MSMB	ENST00000582163.3	c.109+275T>C		intron_variant	Intron 2 of 3	1	NM_002443.4	ENSP00000463092.1
MSMB	ENST00000581478.5	c.109+275T>C		intron_variant	Intron 2 of 2	1		ENSP00000462641.1
MSMB	ENST00000663171.1	c.109+275T>C		intron_variant	Intron 3 of 4			ENSP00000499419.1

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39750 AN: 151984 Hom.: 6608 Cov.: 32

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.262 AC: 39795 AN: 152102 Hom.: 6615 Cov.: 32 AF XY: 0.258 AC XY: 19183 AN XY: 74362

African (AFR) AF: 0.484 AC: 20054 AN: 41450

American (AMR) AF: 0.199 AC: 3039 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 678 AN: 3470

East Asian (EAS) AF: 0.161 AC: 834 AN: 5172

South Asian (SAS) AF: 0.146 AC: 705 AN: 4820

European-Finnish (FIN) AF: 0.219 AC: 2316 AN: 10590

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11523 AN: 67998

Other (OTH) AF: 0.242 AC: 511 AN: 2110

Alfa AF: 0.216 Hom.: 565

Bravo AF: 0.270

Asia WGS AF: 0.206 AC: 713 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.053
DANN	Benign	0.42
PhyloP100		-3.6

Splicing

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

Other links and lift over

dbSNP: rs2075894; hg19: chr10-51556111;