Genetic Variant MSMB:c.-52T>G (chr10-46046289-A-C) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_StrongBS2

The ENST00000663171.1(MSMB):c.-52T>G variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0108 in 1,579,506 control chromosomes in the GnomAD database, including 99 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 0.0076 ( 6 hom., cov: 34)

Exomes 𝑓: 0.011 ( 93 hom. )

Consequence

MSMB
ENST00000663171.1 5_prime_UTR_premature_start_codon_gain

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.588

Publications

9 publications found

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]

MSMB links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BS2

High Homozygotes in GnomAd4 at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MSMB	NM_002443.4 link	c.-52T>G		upstream_gene_variant		ENST00000582163.3	NP_002434.1	P08118-1
MSMB	NM_138634.3 link	c.-52T>G		upstream_gene_variant			NP_619540.1	P08118-2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
MSMB	ENST00000663171.1 link	c.-52T>G	5_prime_UTR_premature_start_codon_gain_variant	Exon 2 of 5			ENSP00000499419.1	A0A590UJG9
MSMB	ENST00000663171.1 link	c.-52T>G	5_prime_UTR_variant	Exon 2 of 5			ENSP00000499419.1	A0A590UJG9
MSMB	ENST00000582163.3 link	c.-52T>G	upstream_gene_variant		1	NM_002443.4	ENSP00000463092.1	P08118-1
MSMB	ENST00000581478.5 link	c.-52T>G	upstream_gene_variant		1		ENSP00000462641.1	P08118-2

Frequencies

GnomAD3 genomes

AF:

0.00759

AC:

1155

AN:

152232

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00265

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.00550

Gnomad ASJ

AF:

0.0216

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00104

Gnomad FIN

AF:

0.00358

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0121

Gnomad OTH

AF:

0.00766

GnomAD4 exome

AF:

0.0111

AC:

15859

AN:

1427156

Hom.:

Cov.:

AF XY:

0.0108

AC XY:

7696

AN XY:

712332

show subpopulations

African (AFR)

AF:

0.00158

AC:

AN:

32872

American (AMR)

AF:

0.00645

AC:

287

AN:

44498

Ashkenazi Jewish (ASJ)

AF:

0.0189

AC:

489

AN:

25884

East Asian (EAS)

AF:

0.00

AC:

AN:

39500

South Asian (SAS)

AF:

0.00171

AC:

146

AN:

85258

European-Finnish (FIN)

AF:

0.00611

AC:

326

AN:

53386

Middle Eastern (MID)

AF:

0.00367

AC:

AN:

5716

European-Non Finnish (NFE)

AF:

0.0129

AC:

13932

AN:

1080816

Other (OTH)

AF:

0.0102

AC:

606

AN:

59226

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.480

Heterozygous variant carriers

712

1424

2137

2849

3561

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

518

1036

1554

2072

2590

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00758

AC:

1155

AN:

152350

Hom.:

Cov.:

AF XY:

0.00701

AC XY:

522

AN XY:

74502

show subpopulations

African (AFR)

AF:

0.00264

AC:

110

AN:

41594

American (AMR)

AF:

0.00549

AC:

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.0216

AC:

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5182

South Asian (SAS)

AF:

0.00104

AC:

AN:

4824

European-Finnish (FIN)

AF:

0.00358

AC:

AN:

10622

Middle Eastern (MID)

AF:

0.00340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0121

AC:

825

AN:

68036

Other (OTH)

AF:

0.00758

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

129

194

258

323

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0119

Hom.:

Bravo

AF:

0.00829

Asia WGS

AF:

0.00144

AC:

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

0.40

(source)

DANN

Benign

0.81

PhyloP100

-0.59

PromoterAI

0.025

Neutral

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over