rs7904463

Variant names:

• chr10-46036353-G-A
• rs7904463
• NM_002443.4:c.215+2613C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-46036353-G-A
• chr10-46036353-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 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=-0.89).
• 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 rank	MANE	Protein	UniProt
MSMB	NM_002443.4	c.215+2613C>T		intron_variant	Intron 3 of 3	ENST00000582163.3	NP_002434.1
MSMB	NM_138634.3	c.110-2802C>T		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.215+2613C>T		intron_variant	Intron 3 of 3	1	NM_002443.4	ENSP00000463092.1
MSMB	ENST00000581478.5	c.110-2802C>T		intron_variant	Intron 2 of 2	1		ENSP00000462641.1
MSMB	ENST00000663171.1	c.215+2613C>T		intron_variant	Intron 4 of 4			ENSP00000499419.1

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

African (AFR) AF: 0.678 AC: 28124 AN: 41496

American (AMR) AF: 0.337 AC: 5142 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1301 AN: 3472

East Asian (EAS) AF: 0.316 AC: 1630 AN: 5162

South Asian (SAS) AF: 0.339 AC: 1633 AN: 4814

European-Finnish (FIN) AF: 0.297 AC: 3146 AN: 10580

Middle Eastern (MID) AF: 0.353 AC: 103 AN: 292

European-Non Finnish (NFE) AF: 0.327 AC: 22238 AN: 67992

Other (OTH) AF: 0.396 AC: 837 AN: 2112

Alfa AF: 0.342 Hom.: 8016

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
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs7904463; hg19: chr10-51559469;