chr9-132884256-C-T

Variant names:

• chr9-132884256-C-T
• rs2231405
• NM_001316897.2:c.144+165C>T

Variant summary

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

The NM_001316897.2(SPACA9):​c.144+165C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0162 in 152,300 control chromosomes in the GnomAD database, including 70 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 0.016 (70 hom., cov: 32)
• Consequence: SPACA9 NM_001316897.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.644
• Publications: 0 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 (AFR) allele frequency at 95% confidence interval = 0.0549 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPACA9	NM_001316897.2	MANE Select	c.144+165C>T		intron	N/A	NP_001303826.1	Q96E40-1
	SPACA9	NM_001316898.2		c.144+165C>T		intron	N/A	NP_001303827.1	Q96E40-1
	SPACA9	NM_018956.5		c.144+165C>T		intron	N/A	NP_061829.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPACA9	ENST00000356311.10	TSL:2 MANE Select	c.144+165C>T		intron	N/A	ENSP00000348659.5	Q96E40-1
	SPACA9	ENST00000372136.7	TSL:1	c.144+165C>T		intron	N/A	ENSP00000361209.3	Q96E40-1
	SPACA9	ENST00000350499.6	TSL:1	c.144+165C>T		intron	N/A	ENSP00000298546.7	Q96E40-2

Frequencies

GnomAD3 genomes AF: 0.0162 AC: 2466 AN: 152182 Hom.: 70 Cov.: 32

Gnomad AFR AF: 0.0568

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00504

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000147

Gnomad OTH AF: 0.0110

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

GnomAD4 genome AF: 0.0162 AC: 2472 AN: 152300 Hom.: 70 Cov.: 32 AF XY: 0.0160 AC XY: 1192 AN XY: 74486

African (AFR) AF: 0.0568 AC: 2360 AN: 41542

American (AMR) AF: 0.00503 AC: 77 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5188

South Asian (SAS) AF: 0.000415 AC: 2 AN: 4822

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10628

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000147 AC: 10 AN: 68034

Other (OTH) AF: 0.0109 AC: 23 AN: 2110

Alfa AF: 0.00925 Hom.: 22

Bravo AF: 0.0181

Asia WGS AF: 0.00433 AC: 15 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	3.9
DANN	Benign	0.76
PhyloP100		0.64
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs2231405; hg19: chr9-135759643;