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rs10993994

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000663171.1(MSMB):c.-89T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 1,161,688 control chromosomes in the GnomAD database, including 200,462 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 0.54 ( 22862 hom., cov: 33)
Exomes 𝑓: 0.59 ( 177600 hom. )

Consequence

MSMB
ENST00000663171.1 5_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0490
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MSMBENST00000663171.1 linkuse as main transcriptc.-89T>C 5_prime_UTR_variant 2/5

Frequencies

GnomAD3 genomes
AF:
0.538
AC:
81774
AN:
151992
Hom.:
22866
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.390
Gnomad AMI
AF:
0.549
Gnomad AMR
AF:
0.593
Gnomad ASJ
AF:
0.516
Gnomad EAS
AF:
0.540
Gnomad SAS
AF:
0.413
Gnomad FIN
AF:
0.646
Gnomad MID
AF:
0.380
Gnomad NFE
AF:
0.609
Gnomad OTH
AF:
0.535
GnomAD4 exome
AF:
0.587
AC:
593099
AN:
1009578
Hom.:
177600
AF XY:
0.580
AC XY:
302844
AN XY:
521818
show subpopulations
Gnomad4 AFR exome
AF:
0.373
Gnomad4 AMR exome
AF:
0.659
Gnomad4 ASJ exome
AF:
0.507
Gnomad4 EAS exome
AF:
0.546
Gnomad4 SAS exome
AF:
0.427
Gnomad4 FIN exome
AF:
0.650
Gnomad4 NFE exome
AF:
0.612
Gnomad4 OTH exome
AF:
0.554
GnomAD4 genome
AF:
0.538
AC:
81778
AN:
152110
Hom.:
22862
Cov.:
33
AF XY:
0.536
AC XY:
39875
AN XY:
74348
show subpopulations
Gnomad4 AFR
AF:
0.390
Gnomad4 AMR
AF:
0.593
Gnomad4 ASJ
AF:
0.516
Gnomad4 EAS
AF:
0.539
Gnomad4 SAS
AF:
0.412
Gnomad4 FIN
AF:
0.646
Gnomad4 NFE
AF:
0.609
Gnomad4 OTH
AF:
0.529
Alfa
AF:
0.584
Hom.:
52172
Bravo
AF:
0.534
Asia WGS
AF:
0.435
AC:
1513
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
Cadd
Benign
2.3
Dann
Benign
0.60

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10993994; hg19: chr10-51549496; API