rs2519760

Positions:

• chr9-132883034-G-A
• chr9-132883034-G-C
• chr9-132883034-G-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SPACA9	NM_001316897.2	c.-37-877G>A		intron_variant		ENST00000356311.10	NP_001303826.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPACA9	ENST00000356311.10	c.-37-877G>A		intron_variant		2	NM_001316897.2	ENSP00000348659	P3
SPACA9	ENST00000350499.6	c.-37-877G>A		intron_variant		1		ENSP00000298546	A1
SPACA9	ENST00000372136.7	c.-37-877G>A		intron_variant		1		ENSP00000361209	P3

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

Gnomad4 AFR AF: 0.469

Gnomad4 AMR AF: 0.597

Gnomad4 ASJ AF: 0.690

Gnomad4 EAS AF: 0.414

Gnomad4 SAS AF: 0.656

Gnomad4 FIN AF: 0.533

Gnomad4 NFE AF: 0.566

Gnomad4 OTH AF: 0.550

Alfa AF: 0.563 Hom.: 13236

Bravo AF: 0.538

Asia WGS AF: 0.572 AC: 1990 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	1.7
DANN	Benign	0.44

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

Publications

LitVar

Other links and lift over

dbSNP: rs2519760; hg19: chr9-135758421;