chr10-46039373-T-C

Position:

• chr10-46039373-T-C

Variant summary

Our verdict is Benign. Variant got -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

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=-0.96).
• 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/exons	MANE	Protein	UniProt
MSMB	NM_002443.4	c.110-302A>G		intron_variant		ENST00000582163.3	NP_002434.1
MSMB	NM_138634.3	c.109+613A>G		intron_variant			NP_619540.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MSMB	ENST00000582163.3	c.110-302A>G		intron_variant		1	NM_002443.4	ENSP00000463092.1
MSMB	ENST00000581478.5	c.109+613A>G		intron_variant		1		ENSP00000462641.1
MSMB	ENST00000663171.1	c.110-302A>G		intron_variant				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

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.0992

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.156

Alfa AF: 0.147 Hom.: 2338

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2072701; hg19: chr10-51556449;