rs28958

Variant names:

• chr17-32997639-T-C
• rs28958
• NM_173847.5:c.582-73T>C

Your query was ambiguous. Multiple possible variants found:

• chr17-32997639-T-C
• chr17-32997639-T-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.582-73T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 1,557,224 control chromosomes in the GnomAD database, including 136,857 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 0.48 (19042 hom., cov: 31)
  • Exomes 𝑓: 0.40 (117815 hom.)
• Consequence: SPACA3 NM_173847.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.382
• Publications: 11 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.702 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.582-73T>C		intron	N/A	NP_776246.1
	SPACA3	NM_001317225.2		c.306-73T>C		intron	N/A	NP_001304154.1
	SPACA3	NM_001317226.2		c.273-73T>C		intron	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.582-73T>C		intron	N/A	ENSP00000269053.3
	SPACA3	ENST00000580599.5	TSL:1	c.375-73T>C		intron	N/A	ENSP00000463386.1
	SPACA3	ENST00000394637.2	TSL:1	n.725-73T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.477 AC: 72467 AN: 151798 Hom.: 19004 Cov.: 31

Gnomad AFR AF: 0.709

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.452

GnomAD4 exome AF: 0.402 AC: 564885 AN: 1405308 Hom.: 117815 Cov.: 24 AF XY: 0.405 AC XY: 284846 AN XY: 702510

African (AFR) AF: 0.720 AC: 23151 AN: 32174

American (AMR) AF: 0.269 AC: 12009 AN: 44574

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 8659 AN: 25774

East Asian (EAS) AF: 0.458 AC: 18048 AN: 39378

South Asian (SAS) AF: 0.548 AC: 46544 AN: 85004

European-Finnish (FIN) AF: 0.411 AC: 21868 AN: 53206

Middle Eastern (MID) AF: 0.474 AC: 2682 AN: 5658

European-Non Finnish (NFE) AF: 0.384 AC: 407332 AN: 1060982

Other (OTH) AF: 0.420 AC: 24592 AN: 58558

GnomAD4 genome AF: 0.478 AC: 72550 AN: 151916 Hom.: 19042 Cov.: 31 AF XY: 0.479 AC XY: 35573 AN XY: 74264

African (AFR) AF: 0.709 AC: 29376 AN: 41430

American (AMR) AF: 0.342 AC: 5230 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1184 AN: 3468

East Asian (EAS) AF: 0.440 AC: 2254 AN: 5128

South Asian (SAS) AF: 0.556 AC: 2668 AN: 4796

European-Finnish (FIN) AF: 0.417 AC: 4410 AN: 10568

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.382 AC: 25962 AN: 67950

Other (OTH) AF: 0.457 AC: 960 AN: 2100

Alfa AF: 0.420 Hom.: 31866

Bravo AF: 0.476

Asia WGS AF: 0.543 AC: 1885 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.3
DANN	Benign	0.81
PhyloP100		-0.38
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs28958; hg19: chr17-31324657;