11-124694439-A-C

Variant names:

• chr11-124694439-A-C
• rs1378075037
• NM_017425.4:c.449A>C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_017425.4(SPA17):​c.449A>C​(p.Asn150Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000481 in 1,456,784 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000048 (0 hom.)
• Consequence: SPA17 NM_017425.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.0320

Genes affected

SPA17 (HGNC:11210): (sperm autoantigenic protein 17) This gene encodes a protein present at the cell surface. The N-terminus has sequence similarity to human cAMP-dependent protein kinase A (PKA) type II alpha regulatory subunit (RIIa) while the C-terminus has an IQ calmodulin-binding motif. The central portion of the protein has carbohydrate binding motifs and likely functions in cell-cell adhesion. The protein was initially characterized by its involvement in the binding of sperm to the zona pellucida of the oocyte. Recent studies indicate that it is also involved in additional cell-cell adhesion functions such as immune cell migration and metastasis. A retrotransposed pseudogene is present on chromosome 10q22.[provided by RefSeq, Jan 2009]

SIAE (HGNC:18187): (sialic acid acetylesterase) This gene encodes an enzyme which removes 9-O-acetylation modifications from sialic acids. Mutations in this gene are associated with susceptibility to autoimmune disease 6. Multiple transcript variants encoding different isoforms, found either in the cytosol or in the lysosome, have been found for this gene.[provided by RefSeq, Feb 2011]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.056250483).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPA17	NM_017425.4	c.449A>C	p.Asn150Thr	missense_variant	Exon 5 of 5	ENST00000227135.7	NP_059121.1
SPA17	XM_011542870.3	c.449A>C	p.Asn150Thr	missense_variant	Exon 5 of 5		XP_011541172.1
SPA17	XM_024448583.2	c.449A>C	p.Asn150Thr	missense_variant	Exon 5 of 5		XP_024304351.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPA17	ENST00000227135.7	c.449A>C	p.Asn150Thr	missense_variant	Exon 5 of 5	1	NM_017425.4	ENSP00000227135.2
SPA17	ENST00000532692.1	c.449A>C	p.Asn150Thr	missense_variant	Exon 4 of 4	1		ENSP00000432305.1
SPA17	ENST00000524614.1	n.400A>C		non_coding_transcript_exon_variant	Exon 4 of 5	3
SIAE	ENST00000525730.1	n.182T>G		non_coding_transcript_exon_variant	Exon 2 of 4	4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.00000405 AC: 1 AN: 246868 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 133322

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0000552

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000481 AC: 7 AN: 1456784 Hom.: 0 Cov.: 30 AF XY: 0.00000829 AC XY: 6 AN XY: 724194

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.000101

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.01e-7

Gnomad4 OTH exome AF: 0.0000332

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Oct 12, 2024

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.449A>C (p.N150T) alteration is located in exon 5 (coding exon 4) of the SPA17 gene. This alteration results from a A to C substitution at nucleotide position 449, causing the asparagine (N) at amino acid position 150 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.067
BayesDel_addAF	Benign	-0.36	T
BayesDel_noAF	Benign	-0.59
CADD	Benign	6.7
DANN	Benign	0.94
DEOGEN2	Benign	0.016	T;T
Eigen	Benign	-0.84
Eigen_PC	Benign	-0.88
FATHMM_MKL	Benign	0.023	N
LIST_S2	Benign	0.39	.;T
M_CAP	Benign	0.0041	T
MetaRNN	Benign	0.056	T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.69	N;N
PrimateAI	Benign	0.42	T
PROVEAN	Benign	-0.88	N;N
REVEL	Benign	0.022
Sift	Uncertain	0.0090	D;D
Sift4G	Benign	0.41	T;T
Polyphen		0.028	B;B
Vest4		0.096
MutPred		0.23		Gain of phosphorylation at N150 (P = 0.0019);Gain of phosphorylation at N150 (P = 0.0019);
MVP		0.15
MPC		0.021
ClinPred		0.066	T
GERP RS		2.4
Varity_R		0.071
gMVP		0.027

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1378075037; hg19: chr11-124564335;