rs9904938

Variant names:

• chr17-32974460-C-T
• rs9904938
• ENST00000580599.5:c.-291-1367C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPACA3	ENST00000580599.5	c.-291-1367C>T		intron_variant	Intron 1 of 5	1		ENSP00000463386.1

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

African (AFR) AF: 0.187 AC: 7749 AN: 41466

American (AMR) AF: 0.0461 AC: 704 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0187 AC: 65 AN: 3472

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5178

South Asian (SAS) AF: 0.0415 AC: 200 AN: 4816

European-Finnish (FIN) AF: 0.0621 AC: 657 AN: 10586

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0482 AC: 3280 AN: 67998

Other (OTH) AF: 0.0555 AC: 117 AN: 2108

Alfa AF: 0.0567 Hom.: 190

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
PhyloP100		0.055
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs9904938; hg19: chr17-31301478;