rs1037675

Variant names:

• chr7-50119761-G-A
• rs1037675
• NM_001161834.3:c.652-9956G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001161834.3(SPMIP7):​c.652-9956G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.837 in 152,180 control chromosomes in the GnomAD database, including 53,293 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 0.84 (53293 hom., cov: 33)
• Consequence: SPMIP7 NM_001161834.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.612
• Publications: 1 publications found

Genes affected

SPMIP7 (HGNC:22564): (sperm microtubule inner protein 7)

ZPBP (HGNC:15662): (zona pellucida binding protein) ZPBP is one of several proteins that are thought to participate in secondary binding between acrosome-reacted sperm and the egg-specific extracellular matrix, the zona pellucida (McLeskey et al., 1998 [PubMed 9378618]).[supplied by OMIM, Aug 2008]

ZPBP Gene-Disease associations (from GenCC):

• spermatogenic failure 66

  Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001161834.3. 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
	SPMIP7	NM_001161834.3	MANE Select	c.652-9956G>A		intron	N/A	NP_001155306.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPMIP7	ENST00000297001.7	TSL:5 MANE Select	c.652-9956G>A		intron	N/A	ENSP00000297001.7
	ZPBP	ENST00000450231.1	TSL:3	c.-158+447C>T		intron	N/A	ENSP00000390054.1

Frequencies

GnomAD3 genomes AF: 0.836 AC: 127188 AN: 152062 Hom.: 53236 Cov.: 33

Gnomad AFR AF: 0.833

Gnomad AMI AF: 0.911

Gnomad AMR AF: 0.859

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.924

Gnomad SAS AF: 0.799

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.840

Gnomad OTH AF: 0.814

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.837 AC: 127304 AN: 152180 Hom.: 53293 Cov.: 33 AF XY: 0.835 AC XY: 62101 AN XY: 74412

African (AFR) AF: 0.833 AC: 34574 AN: 41510

American (AMR) AF: 0.859 AC: 13120 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.770 AC: 2674 AN: 3472

East Asian (EAS) AF: 0.924 AC: 4788 AN: 5184

South Asian (SAS) AF: 0.800 AC: 3855 AN: 4820

European-Finnish (FIN) AF: 0.795 AC: 8427 AN: 10596

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.839 AC: 57090 AN: 68006

Other (OTH) AF: 0.816 AC: 1724 AN: 2114

Alfa AF: 0.836 Hom.: 6866

Bravo AF: 0.841

Asia WGS AF: 0.865 AC: 3006 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.72
DANN	Benign	0.22
PhyloP100		-0.61
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1037675; hg19: chr7-50159357;