NM_001316897.2:c.-38+452G>C

Variant names:

• chr9-132879466-G-C
• rs2519759
• NM_001316897.2:c.-38+452G>C

Variant summary

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

The NM_001316897.2(SPACA9):​c.-38+452G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.732 in 152,074 control chromosomes in the GnomAD database, including 41,135 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 0.73 (41135 hom., cov: 32)
• Consequence: SPACA9 NM_001316897.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900
• Publications: 1 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.84 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.-38+452G>C		intron	N/A	NP_001303826.1
	SPACA9	NM_001316898.2		c.-38+1030G>C		intron	N/A	NP_001303827.1
	SPACA9	NM_018956.5		c.-38+452G>C		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.-38+452G>C		intron	N/A	ENSP00000348659.5
	SPACA9	ENST00000372136.7	TSL:1	c.-38+1030G>C		intron	N/A	ENSP00000361209.3
	SPACA9	ENST00000350499.6	TSL:1	c.-38+452G>C		intron	N/A	ENSP00000298546.7

Frequencies

GnomAD3 genomes AF: 0.732 AC: 111301 AN: 151956 Hom.: 41114 Cov.: 32

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.703

Gnomad AMR AF: 0.715

Gnomad ASJ AF: 0.800

Gnomad EAS AF: 0.855

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.818

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.717

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

GnomAD4 genome AF: 0.732 AC: 111367 AN: 152074 Hom.: 41135 Cov.: 32 AF XY: 0.737 AC XY: 54789 AN XY: 74346

African (AFR) AF: 0.629 AC: 26048 AN: 41436

American (AMR) AF: 0.715 AC: 10938 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.800 AC: 2776 AN: 3472

East Asian (EAS) AF: 0.854 AC: 4419 AN: 5172

South Asian (SAS) AF: 0.862 AC: 4154 AN: 4818

European-Finnish (FIN) AF: 0.818 AC: 8659 AN: 10592

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.765 AC: 52009 AN: 67984

Other (OTH) AF: 0.720 AC: 1517 AN: 2106

Alfa AF: 0.720 Hom.: 2525

Bravo AF: 0.717

Asia WGS AF: 0.851 AC: 2958 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.43
PhyloP100		0.0090
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: rs2519759; hg19: chr9-135754853;