rs9895463

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000580599.5(SPACA3):​c.-174+9565A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 151,976 control chromosomes in the GnomAD database, including 20,505 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 0.51 ( 20505 hom., cov: 32)

Consequence

SPACA3
ENST00000580599.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.365
Variant links:
Genes affected
SPACA3 (HGNC:16260): (sperm acrosome associated 3) The protein encoded by this gene is a sperm surface protein that may be involved in adhesion to the egg prior to fertilization. While the encoded protein has significant similarity to lysozyme at the amino acid level, it has no detectable bacteriocidal activity. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2015]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SPACA3ENST00000580599.5 linkuse as main transcriptc.-174+9565A>G intron_variant 1 ENSP00000463386 P2Q8IXA5-2

Frequencies

GnomAD3 genomes
AF:
0.513
AC:
77914
AN:
151858
Hom.:
20493
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.620
Gnomad AMI
AF:
0.552
Gnomad AMR
AF:
0.486
Gnomad ASJ
AF:
0.419
Gnomad EAS
AF:
0.411
Gnomad SAS
AF:
0.412
Gnomad FIN
AF:
0.473
Gnomad MID
AF:
0.329
Gnomad NFE
AF:
0.481
Gnomad OTH
AF:
0.488
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.513
AC:
77946
AN:
151976
Hom.:
20505
Cov.:
32
AF XY:
0.511
AC XY:
37932
AN XY:
74296
show subpopulations
Gnomad4 AFR
AF:
0.620
Gnomad4 AMR
AF:
0.486
Gnomad4 ASJ
AF:
0.419
Gnomad4 EAS
AF:
0.411
Gnomad4 SAS
AF:
0.411
Gnomad4 FIN
AF:
0.473
Gnomad4 NFE
AF:
0.481
Gnomad4 OTH
AF:
0.487
Alfa
AF:
0.471
Hom.:
9021
Bravo
AF:
0.519
Asia WGS
AF:
0.423
AC:
1473
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.84
DANN
Benign
0.49

Splicing

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.

Other links and lift over

dbSNP: rs9895463; hg19: chr17-31312527; API