Variant X-14914498-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_152581.4(MOSPD2):c.993-5C>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00102 in 1,153,112 control chromosomes in the GnomAD database, including 9 homozygotes. There are 273 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0051 ( 6 hom., 143 hem., cov: 23)

Exomes 𝑓: 0.00058 ( 3 hom. 130 hem. )

Consequence

MOSPD2
NM_152581.4 splice_region, intron

Scores

Splicing: ADA: 0.006834

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.390

Variant links:

Genes affected

MOSPD2 (HGNC:28381): (motile sperm domain containing 2) Involved in positive regulation of monocyte chemotaxis and positive regulation of neutrophil chemotaxis. Located in endoplasmic reticulum and endoplasmic reticulum-endosome membrane contact site. Is integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

MOSPD2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant X-14914498-C-A is Benign according to our data. Variant chrX-14914498-C-A is described in ClinVar as [Benign]. Clinvar id is 712020.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00512 (570/111225) while in subpopulation AFR AF= 0.0174 (534/30643). AF 95% confidence interval is 0.0162. There are 6 homozygotes in gnomad4. There are 143 alleles in male gnomad4 subpopulation. Median coverage is 23. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 6 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
MOSPD2	NM_152581.4 link	c.993-5C>A	splice_region_variant, intron_variant	ENST00000380492.8	NP_689794.1	Q8NHP6-1
MOSPD2	NM_001330241.2 link	c.993-5C>A	splice_region_variant, intron_variant		NP_001317170.1	R4GMN1
MOSPD2	NM_001177475.2 link	c.804-5C>A	splice_region_variant, intron_variant		NP_001170946.1	Q8NHP6-2

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
MOSPD2	ENST00000380492.8 link	c.993-5C>A	splice_region_variant, intron_variant	1	NM_152581.4	ENSP00000369860.3	Q8NHP6-1
MOSPD2	ENST00000482354.5 link	c.993-5C>A	splice_region_variant, intron_variant	5		ENSP00000473271.1	R4GMN1
MOSPD2	ENST00000460386.1 link	c.354-5C>A	splice_region_variant, intron_variant	5		ENSP00000473379.1	R4GMW5
MOSPD2	ENST00000495110.1 link	n.1081-5C>A	splice_region_variant, intron_variant	2

Frequencies

GnomAD3 genomes

AF:

0.00513

AC:

570

AN:

111176

Hom.:

Cov.:

AF XY:

0.00428

AC XY:

143

AN XY:

33442

show subpopulations

Gnomad AFR

AF:

0.0175

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00210

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000742

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00418

Gnomad NFE

AF:

0.0000756

Gnomad OTH

AF:

0.00467

GnomAD3 exomes

AF:

0.00163

AC:

267

AN:

163615

Hom.:

AF XY:

0.000830

AC XY:

AN XY:

53021

show subpopulations

Gnomad AFR exome

AF:

0.0187

Gnomad AMR exome

AF:

0.00132

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000105

Gnomad OTH exome

AF:

0.000760

GnomAD4 exome

AF:

0.000582

AC:

606

AN:

1041887

Hom.:

Cov.:

AF XY:

0.000405

AC XY:

130

AN XY:

321055

show subpopulations

Gnomad4 AFR exome

AF:

0.0182

Gnomad4 AMR exome

AF:

0.00147

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000401

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000275

Gnomad4 OTH exome

AF:

0.00186

GnomAD4 genome

AF:

0.00512

AC:

570

AN:

111225

Hom.:

Cov.:

AF XY:

0.00427

AC XY:

143

AN XY:

33501

show subpopulations

Gnomad4 AFR

AF:

0.0174

Gnomad4 AMR

AF:

0.00210

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000745

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000756

Gnomad4 OTH

AF:

0.00461

Alfa

AF:

0.000325

Hom.:

Bravo

AF:

0.00607

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Mar 29, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

3.7

DANN

Benign

0.42

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.0068

dbscSNV1_RF

Benign

0.092

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

LitVar

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

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over