rs7904463

chr10-46036353-G-Achr10-46036353-G-T

Variant summary

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

The NM_002443.4(MSMB):c.215+2613C>T 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 152,106 control chromosomes in the GnomAD database, including 15,560 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 (15560 hom., cov: 33)
• Consequence: MSMB NM_002443.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.637

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MSMB	NM_002443.4	c.215+2613C>T		intron_variant		ENST00000582163.3
MSMB	NM_138634.3	c.110-2802C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MSMB	ENST00000582163.3	c.215+2613C>T		intron_variant		1	NM_002443.4	P1
MSMB	ENST00000581478.5	c.110-2802C>T		intron_variant		1
MSMB	ENST00000663171.1	c.215+2613C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64359 AN: 151988 Hom.: 15528 Cov.: 33

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.360

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: 64429 AN: 152106 Hom.: 15560 Cov.: 33 AF XY: 0.419 AC XY: 31124 AN XY: 74362

Gnomad4 AFR AF: 0.678

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.375

Gnomad4 EAS AF: 0.316

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.327

Gnomad4 OTH AF: 0.396

Alfa AF: 0.338 Hom.: 6861

Bravo AF: 0.436

Asia WGS AF: 0.359 AC: 1249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.9
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7904463; hg19: chr10-51559469;