rs9904938

Positions:

• chr17-32974460-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000580599.5(SPACA3):​c.-291-1367C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0844 in 152,106 control chromosomes in the GnomAD database, including 933 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 0.084 (933 hom., cov: 31)
• Consequence: SPACA3 ENST00000580599.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPACA3	ENST00000580599.5	c.-291-1367C>T		intron_variant		1		P2

Frequencies

GnomAD3 genomes AF: 0.0844 AC: 12825 AN: 151988 Hom.: 930 Cov.: 31

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.0560

Gnomad AMR AF: 0.0461

Gnomad ASJ AF: 0.0187

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0421

Gnomad FIN AF: 0.0621

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0482

Gnomad OTH AF: 0.0561

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

GnomAD4 genome AF: 0.0844 AC: 12831 AN: 152106 Hom.: 933 Cov.: 31 AF XY: 0.0822 AC XY: 6110 AN XY: 74354

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.0461

Gnomad4 ASJ AF: 0.0187

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0415

Gnomad4 FIN AF: 0.0621

Gnomad4 NFE AF: 0.0482

Gnomad4 OTH AF: 0.0555

Alfa AF: 0.0561 Hom.: 163

Bravo AF: 0.0866

Asia WGS AF: 0.0350 AC: 122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.3
DANN	Benign	0.52

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9904938; hg19: chr17-31301478;