Variant rs2073869 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001316897.2(SPACA9):c.487C>T(p.Leu163=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 1,613,394 control chromosomes in the GnomAD database, including 26,454 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 0.19 ( 2791 hom., cov: 32)

Exomes 𝑓: 0.18 ( 23663 hom. )

Consequence

SPACA9
NM_001316897.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.126

Variant links:

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]

SPACA9 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP7

Synonymous conserved (PhyloP=0.126 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPACA9	NM_001316897.2 linkuse as main transcript	c.487C>T	p.Leu163=	synonymous_variant	4/4	ENST00000356311.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPACA9	ENST00000356311.10 linkuse as main transcript	c.487C>T	p.Leu163=	synonymous_variant	4/4	2	NM_001316897.2	P3	Q96E40-1
SPACA9	ENST00000372136.7 linkuse as main transcript	c.487C>T	p.Leu163=	synonymous_variant	4/4	1		P3	Q96E40-1
SPACA9	ENST00000350499.6 linkuse as main transcript	c.487C>T	p.Leu163=	synonymous_variant	4/5	1		A1	Q96E40-2

Frequencies

GnomAD3 genomes

AF:

0.188

AC:

28533

AN:

151938

Hom.:

2789

Cov.:

show subpopulations

Gnomad AFR

AF:

0.198

Gnomad AMI

AF:

0.109

Gnomad AMR

AF:

0.130

Gnomad ASJ

AF:

0.118

Gnomad EAS

AF:

0.253

Gnomad SAS

AF:

0.186

Gnomad FIN

AF:

0.280

Gnomad MID

AF:

0.184

Gnomad NFE

AF:

0.181

Gnomad OTH

AF:

0.174

GnomAD3 exomes

AF:

0.185

AC:

46066

AN:

249156

Hom.:

4541

AF XY:

0.184

AC XY:

24813

AN XY:

134896

show subpopulations

Gnomad AFR exome

AF:

0.202

Gnomad AMR exome

AF:

0.146

Gnomad ASJ exome

AF:

0.118

Gnomad EAS exome

AF:

0.267

Gnomad SAS exome

AF:

0.173

Gnomad FIN exome

AF:

0.273

Gnomad NFE exome

AF:

0.173

Gnomad OTH exome

AF:

0.184

GnomAD4 exome

AF:

0.177

AC:

258023

AN:

1461334

Hom.:

23663

Cov.:

AF XY:

0.178

AC XY:

129063

AN XY:

726946

show subpopulations

Gnomad4 AFR exome

AF:

0.202

Gnomad4 AMR exome

AF:

0.144

Gnomad4 ASJ exome

AF:

0.116

Gnomad4 EAS exome

AF:

0.252

Gnomad4 SAS exome

AF:

0.176

Gnomad4 FIN exome

AF:

0.274

Gnomad4 NFE exome

AF:

0.172

Gnomad4 OTH exome

AF:

0.176

GnomAD4 genome

AF:

0.188

AC:

28543

AN:

152060

Hom.:

2791

Cov.:

AF XY:

0.190

AC XY:

14095

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.197

Gnomad4 AMR

AF:

0.130

Gnomad4 ASJ

AF:

0.118

Gnomad4 EAS

AF:

0.253

Gnomad4 SAS

AF:

0.187

Gnomad4 FIN

AF:

0.280

Gnomad4 NFE

AF:

0.181

Gnomad4 OTH

AF:

0.173

Alfa

AF:

0.176

Hom.:

3112

Bravo

AF:

0.178

Asia WGS

AF:

0.211

AC:

735

AN:

3478

EpiCase

AF:

0.168

EpiControl

AF:

0.167

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

6.1

DANN

Benign

0.80

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over