rs1033069

chr2-213900484-A-G

Variant summary

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

The NM_024532.5(SPAG16):c.1215-29476A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 151,930 control chromosomes in the GnomAD database, including 27,793 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 0.58 (27793 hom., cov: 32)
• Consequence: SPAG16 NM_024532.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.372

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.818 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPAG16	NM_024532.5	c.1215-29476A>G		intron_variant		ENST00000331683.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPAG16	ENST00000331683.10	c.1215-29476A>G		intron_variant		1	NM_024532.5	P1
SPAG16	ENST00000406979.6	c.*1216-29476A>G		intron_variant, NMD_transcript_variant		1
SPAG16	ENST00000451561.1	c.272+37856A>G		intron_variant		3
SPAG16	ENST00000452556.5	c.*781-29476A>G		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88766 AN: 151812 Hom.: 27775 Cov.: 32

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.890

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.840

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.585 AC: 88830 AN: 151930 Hom.: 27793 Cov.: 32 AF XY: 0.590 AC XY: 43817 AN XY: 74280

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.618

Gnomad4 ASJ AF: 0.561

Gnomad4 EAS AF: 0.559

Gnomad4 SAS AF: 0.839

Gnomad4 FIN AF: 0.671

Gnomad4 NFE AF: 0.685

Gnomad4 OTH AF: 0.567

Alfa AF: 0.672 Hom.: 15520

Bravo AF: 0.567

Asia WGS AF: 0.691 AC: 2403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.67
Dann	Benign	0.25

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1033069; hg19: chr2-214765208;