rs2372227

Positions:

• chr2-214169711-C-A
• chr2-214169711-C-G

Variant summary

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

The NM_024532.5(SPAG16):​c.1720+20445C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 151,952 control chromosomes in the GnomAD database, including 4,881 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 0.24 (4881 hom., cov: 31)
• Consequence: SPAG16 NM_024532.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.74

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=-0.49).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SPAG16	NM_024532.5	c.1720+20445C>A		intron_variant		ENST00000331683.10	NP_078808.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPAG16	ENST00000331683.10	c.1720+20445C>A		intron_variant		1	NM_024532.5	ENSP00000332592	P1

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36406 AN: 151834 Hom.: 4876 Cov.: 31

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.240 AC: 36421 AN: 151952 Hom.: 4881 Cov.: 31 AF XY: 0.233 AC XY: 17328 AN XY: 74246

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.200

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.264

Alfa AF: 0.275 Hom.: 2812

Bravo AF: 0.238

Asia WGS AF: 0.260 AC: 906 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	15
DANN	Benign	0.62

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: rs2372227; hg19: chr2-215034435;