Genetic Variant MOSPD3:c.511+157G>C (chr7-100613863-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_023948.5(MOSPD3):c.511+157G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 708,442 control chromosomes in the GnomAD database, including 12,620 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 0.16 ( 2176 hom., cov: 32)

Exomes 𝑓: 0.19 ( 10444 hom. )

Consequence

MOSPD3
NM_023948.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0460

Publications

6 publications found

Variant links:

Genes affected

MOSPD3 (HGNC:25078): (motile sperm domain containing 3) This gene encodes a multi-pass membrane protein with a major sperm protein (MSP) domain. The deletion of a similar mouse gene is associated with defective cardiac development and neonatal lethality. Alternate transcriptional splice variants, encoding different isoforms, have been described. [provided by RefSeq, Jul 2008]

MOSPD3 links:

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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=-0.86).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_023948.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
MOSPD3	NM_023948.5	MANE Select	c.511+157G>C	intron	N/A	NP_076438.1
MOSPD3	NM_001040097.2		c.511+157G>C	intron	N/A	NP_001035186.1
MOSPD3	NM_001040098.1		c.511+157G>C	intron	N/A	NP_001035187.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
MOSPD3	ENST00000393950.7	TSL:1 MANE Select	c.511+157G>C	intron	N/A	ENSP00000377522.2
MOSPD3	ENST00000424091.2	TSL:1	c.481+157G>C	intron	N/A	ENSP00000404626.2
MOSPD3	ENST00000223054.8	TSL:2	c.511+157G>C	intron	N/A	ENSP00000223054.4

Frequencies

GnomAD3 genomes

AF:

0.158

AC:

24054

AN:

152098

Hom.:

2172

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0771

Gnomad AMI

AF:

0.200

Gnomad AMR

AF:

0.151

Gnomad ASJ

AF:

0.184

Gnomad EAS

AF:

0.111

Gnomad SAS

AF:

0.152

Gnomad FIN

AF:

0.219

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.202

Gnomad OTH

AF:

0.147

GnomAD4 exome

AF:

0.188

AC:

104739

AN:

556226

Hom.:

10444

AF XY:

0.187

AC XY:

53938

AN XY:

288118

show subpopulations

African (AFR)

AF:

0.0764

AC:

1101

AN:

14406

American (AMR)

AF:

0.160

AC:

3173

AN:

19884

Ashkenazi Jewish (ASJ)

AF:

0.184

AC:

2682

AN:

14586

East Asian (EAS)

AF:

0.106

AC:

3356

AN:

31698

South Asian (SAS)

AF:

0.163

AC:

7850

AN:

48182

European-Finnish (FIN)

AF:

0.210

AC:

6252

AN:

29708

Middle Eastern (MID)

AF:

0.132

AC:

365

AN:

2758

European-Non Finnish (NFE)

AF:

0.204

AC:

74587

AN:

365354

Other (OTH)

AF:

0.181

AC:

5373

AN:

29650

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

4516

9032

13547

18063

22579

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1194

2388

3582

4776

5970

<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:

0.158

AC:

24067

AN:

152216

Hom.:

2176

Cov.:

AF XY:

0.156

AC XY:

11608

AN XY:

74412

show subpopulations

African (AFR)

AF:

0.0773

AC:

3211

AN:

41544

American (AMR)

AF:

0.151

AC:

2309

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.184

AC:

640

AN:

3472

East Asian (EAS)

AF:

0.111

AC:

574

AN:

5186

South Asian (SAS)

AF:

0.154

AC:

741

AN:

4826

European-Finnish (FIN)

AF:

0.219

AC:

2314

AN:

10582

Middle Eastern (MID)

AF:

0.109

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.202

AC:

13756

AN:

68010

Other (OTH)

AF:

0.146

AC:

308

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1053

2106

3159

4212

5265

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

262

524

786

1048

1310

<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:

0.114

Hom.:

245

Bravo

AF:

0.150

Asia WGS

AF:

0.135

AC:

470

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

2.6

(source)

DANN

Benign

0.44

PhyloP100

0.046

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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