10-46039373-T-C

Variant names:

• chr10-46039373-T-C
• rs2072701
• NM_002443.4:c.110-302A>G

Variant summary

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

The NM_002443.4(MSMB):​c.110-302A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,180 control chromosomes in the GnomAD database, including 1,705 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 0.15 (1705 hom., cov: 33)
• Consequence: MSMB NM_002443.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.83
• Publications: 2 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MSMB	NM_002443.4	c.110-302A>G		intron_variant	Intron 2 of 3	ENST00000582163.3	NP_002434.1
MSMB	NM_138634.3	c.109+613A>G		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.110-302A>G		intron_variant	Intron 2 of 3	1	NM_002443.4	ENSP00000463092.1
MSMB	ENST00000581478.5	c.109+613A>G		intron_variant	Intron 2 of 2	1		ENSP00000462641.1
MSMB	ENST00000663171.1	c.110-302A>G		intron_variant	Intron 3 of 4			ENSP00000499419.1

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22860 AN: 152062 Hom.: 1708 Cov.: 33

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.0912

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.0998

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.150 AC: 22865 AN: 152180 Hom.: 1705 Cov.: 33 AF XY: 0.150 AC XY: 11142 AN XY: 74406

African (AFR) AF: 0.157 AC: 6515 AN: 41536

American (AMR) AF: 0.145 AC: 2222 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 512 AN: 3466

East Asian (EAS) AF: 0.119 AC: 616 AN: 5186

South Asian (SAS) AF: 0.0992 AC: 479 AN: 4828

European-Finnish (FIN) AF: 0.181 AC: 1919 AN: 10586

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10152 AN: 67986

Other (OTH) AF: 0.156 AC: 329 AN: 2106

Alfa AF: 0.148 Hom.: 6038

Bravo AF: 0.147

Asia WGS AF: 0.134 AC: 465 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.013
DANN	Benign	0.39
PhyloP100		-4.8

Splicing

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

Other links and lift over

dbSNP: rs2072701; hg19: chr10-51556449;