rs7812235

chr7-100613863-G-Cchr7-100613863-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0460

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MOSPD3	NM_023948.5	c.511+157G>C		intron_variant		ENST00000393950.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MOSPD3	ENST00000393950.7	c.511+157G>C		intron_variant		1	NM_023948.5	P1

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24054 AN: 152098 Hom.: 2172 Cov.: 32

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

Gnomad4 AFR exome AF: 0.0764

Gnomad4 AMR exome AF: 0.160

Gnomad4 ASJ exome AF: 0.184

Gnomad4 EAS exome AF: 0.106

Gnomad4 SAS exome AF: 0.163

Gnomad4 FIN exome AF: 0.210

Gnomad4 NFE exome AF: 0.204

Gnomad4 OTH exome AF: 0.181

GnomAD4 genome AF: 0.158 AC: 24067 AN: 152216 Hom.: 2176 Cov.: 32 AF XY: 0.156 AC XY: 11608 AN XY: 74412

Gnomad4 AFR AF: 0.0773

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.111

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.146

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	2.6
Dann	Benign	0.44

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

LitVar

Other links and lift over

dbSNP: rs7812235; hg19: chr7-100211486;