9-132883034-G-A

Variant names:

• chr9-132883034-G-A
• rs2519760
• NM_001316897.2:c.-37-877G>A

Variant summary

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

The NM_001316897.2(SPACA9):​c.-37-877G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.541 in 151,864 control chromosomes in the GnomAD database, including 22,574 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 0.54 (22574 hom., cov: 31)
• Consequence: SPACA9 NM_001316897.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.137
• Publications: 6 publications found

Genes affected

SPACA9 (HGNC:1367): (sperm acrosome associated 9) Predicted to enable calcium-dependent protein binding activity. Located in cytoplasmic microtubule. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.637 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001316897.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPACA9	NM_001316897.2	MANE Select	c.-37-877G>A		intron	N/A	NP_001303826.1
	SPACA9	NM_001316898.2		c.-37-877G>A		intron	N/A	NP_001303827.1
	SPACA9	NM_018956.5		c.-37-877G>A		intron	N/A	NP_061829.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPACA9	ENST00000356311.10	TSL:2 MANE Select	c.-37-877G>A		intron	N/A	ENSP00000348659.5
	SPACA9	ENST00000372136.7	TSL:1	c.-37-877G>A		intron	N/A	ENSP00000361209.3
	SPACA9	ENST00000350499.6	TSL:1	c.-37-877G>A		intron	N/A	ENSP00000298546.7

Frequencies

GnomAD3 genomes AF: 0.540 AC: 82014 AN: 151746 Hom.: 22547 Cov.: 31

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.541 AC: 82087 AN: 151864 Hom.: 22574 Cov.: 31 AF XY: 0.543 AC XY: 40319 AN XY: 74202

African (AFR) AF: 0.469 AC: 19422 AN: 41386

American (AMR) AF: 0.597 AC: 9115 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.690 AC: 2389 AN: 3462

East Asian (EAS) AF: 0.414 AC: 2133 AN: 5150

South Asian (SAS) AF: 0.656 AC: 3162 AN: 4822

European-Finnish (FIN) AF: 0.533 AC: 5611 AN: 10536

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.566 AC: 38442 AN: 67936

Other (OTH) AF: 0.550 AC: 1156 AN: 2100

Alfa AF: 0.562 Hom.: 14570

Bravo AF: 0.538

Asia WGS AF: 0.572 AC: 1990 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	1.7
DANN	Benign	0.44
PhyloP100		-0.14
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: rs2519760; hg19: chr9-135758421;