dbSNP rs10994385: MSMB:c.215+65G>C (chr10-46038901-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002443.4(MSMB):c.215+65G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 1,372,806 control chromosomes in the GnomAD database, including 26,674 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 0.26 ( 6247 hom., cov: 32)

Exomes 𝑓: 0.18 ( 20427 hom. )

Consequence

MSMB
NM_002443.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.463

Publications

6 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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002443.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MSMB	NM_002443.4	MANE Select	c.215+65G>C		intron	N/A	NP_002434.1	P08118-1
	MSMB	NM_138634.3		c.109+1085G>C		intron	N/A	NP_619540.1	P08118-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MSMB	ENST00000582163.3	TSL:1 MANE Select	c.215+65G>C	intron	N/A	ENSP00000463092.1	P08118-1
MSMB	ENST00000581478.5	TSL:1	c.109+1085G>C	intron	N/A	ENSP00000462641.1	P08118-2
MSMB	ENST00000663171.1		c.215+65G>C	intron	N/A	ENSP00000499419.1	A0A590UJG9

Frequencies

GnomAD3 genomes

AF:

0.256

AC:

38902

AN:

151956

Hom.:

6242

Cov.:

show subpopulations

Gnomad AFR

AF:

0.468

Gnomad AMI

AF:

0.0910

Gnomad AMR

AF:

0.198

Gnomad ASJ

AF:

0.196

Gnomad EAS

AF:

0.151

Gnomad SAS

AF:

0.146

Gnomad FIN

AF:

0.214

Gnomad MID

AF:

0.174

Gnomad NFE

AF:

0.169

Gnomad OTH

AF:

0.241

GnomAD4 exome

AF:

0.175

AC:

214006

AN:

1220732

Hom.:

20427

AF XY:

0.174

AC XY:

107218

AN XY:

616348

show subpopulations

African (AFR)

AF:

0.473

AC:

12968

AN:

27440

American (AMR)

AF:

0.148

AC:

6185

AN:

41686

Ashkenazi Jewish (ASJ)

AF:

0.195

AC:

4750

AN:

24380

East Asian (EAS)

AF:

0.165

AC:

6054

AN:

36592

South Asian (SAS)

AF:

0.150

AC:

11879

AN:

79130

European-Finnish (FIN)

AF:

0.203

AC:

10600

AN:

52268

Middle Eastern (MID)

AF:

0.153

AC:

806

AN:

5252

European-Non Finnish (NFE)

AF:

0.167

AC:

150814

AN:

901688

Other (OTH)

AF:

0.190

AC:

9950

AN:

52296

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

8506

17012

25519

34025

42531

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4974

9948

14922

19896

24870

<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:

0.256

AC:

38944

AN:

152074

Hom.:

6247

Cov.:

AF XY:

0.252

AC XY:

18739

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.467

AC:

19384

AN:

41466

American (AMR)

AF:

0.197

AC:

3011

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.196

AC:

678

AN:

3468

East Asian (EAS)

AF:

0.151

AC:

781

AN:

5174

South Asian (SAS)

AF:

0.145

AC:

700

AN:

4818

European-Finnish (FIN)

AF:

0.214

AC:

2259

AN:

10558

Middle Eastern (MID)

AF:

0.177

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.169

AC:

11490

AN:

67992

Other (OTH)

AF:

0.240

AC:

506

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

1349

2698

4047

5396

6745

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

386

772

1158

1544

1930

<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:

0.0833

Hom.:

101

Bravo

AF:

0.264

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.46

(source)

DANN

Benign

0.39

PhyloP100

-0.46

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over