rs10490486

chr2-214054387-G-A

Variant summary

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

The NM_024532.5(SPAG16):c.1527+40310G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.085 in 152,152 control chromosomes in the GnomAD database, including 683 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 0.085 (683 hom., cov: 32)
• Consequence: SPAG16 NM_024532.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730

Genes affected

SPAG16 (HGNC:23225): (sperm associated antigen 16) Cilia and flagella are comprised of a microtubular backbone, the axoneme, which is organized by the basal body and surrounded by plasma membrane. SPAG16 encodes 2 major proteins that associate with the axoneme of sperm tail and the nucleus of postmeiotic germ cells, respectively (Zhang et al., 2007 [PubMed 17699735]).[supplied by OMIM, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPAG16	NM_024532.5	c.1527+40310G>A		intron_variant		ENST00000331683.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPAG16	ENST00000331683.10	c.1527+40310G>A		intron_variant		1	NM_024532.5	P1

Frequencies

GnomAD3 genomes AF: 0.0850 AC: 12921 AN: 152034 Hom.: 681 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.0187

Gnomad AMR AF: 0.0736

Gnomad ASJ AF: 0.0743

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.0822

Gnomad FIN AF: 0.0629

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0641

Gnomad OTH AF: 0.0943

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

GnomAD4 genome AF: 0.0850 AC: 12939 AN: 152152 Hom.: 683 Cov.: 32 AF XY: 0.0854 AC XY: 6350 AN XY: 74380

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.0737

Gnomad4 ASJ AF: 0.0743

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.0818

Gnomad4 FIN AF: 0.0629

Gnomad4 NFE AF: 0.0641

Gnomad4 OTH AF: 0.0947

Alfa AF: 0.0692 Hom.: 58

Bravo AF: 0.0895

Asia WGS AF: 0.158 AC: 549 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.8
Dann	Benign	0.60

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: rs10490486; hg19: chr2-214919111;