chr17-32998085-A-G

Variant names:

• chr17-32998085-A-G
• rs757079
• NM_173847.5:c.*307A>G

Variant summary

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

The NM_173847.5(SPACA3):​c.*307A>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 151,928 control chromosomes in the GnomAD database, including 22,534 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 (22534 hom., cov: 31)
• Consequence: SPACA3 NM_173847.5 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.481
• Publications: 3 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.807 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173847.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPACA3	NM_173847.5	MANE Select	c.*307A>G		downstream_gene	N/A	NP_776246.1
	SPACA3	NM_001317225.2		c.*307A>G		downstream_gene	N/A	NP_001304154.1
	SPACA3	NM_001317226.2		c.*307A>G		downstream_gene	N/A	NP_001304155.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPACA3	ENST00000269053.8	TSL:1 MANE Select	c.*307A>G		downstream_gene	N/A	ENSP00000269053.3
	SPACA3	ENST00000580599.5	TSL:1	c.*307A>G		downstream_gene	N/A	ENSP00000463386.1
	SPACA3	ENST00000394637.2	TSL:1	n.*208A>G		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77140 AN: 151810 Hom.: 22471 Cov.: 31

Gnomad AFR AF: 0.814

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.441

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.508 AC: 77255 AN: 151928 Hom.: 22534 Cov.: 31 AF XY: 0.509 AC XY: 37810 AN XY: 74236

African (AFR) AF: 0.815 AC: 33765 AN: 41442

American (AMR) AF: 0.356 AC: 5427 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1184 AN: 3470

East Asian (EAS) AF: 0.440 AC: 2268 AN: 5150

South Asian (SAS) AF: 0.558 AC: 2683 AN: 4804

European-Finnish (FIN) AF: 0.418 AC: 4412 AN: 10548

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.382 AC: 25991 AN: 67952

Other (OTH) AF: 0.481 AC: 1015 AN: 2108

Alfa AF: 0.403 Hom.: 16866

Bravo AF: 0.511

Asia WGS AF: 0.554 AC: 1922 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.6
DANN	Benign	0.81
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs757079; hg19: chr17-31325103;