rs1033069

Variant names:

• chr2-213900484-A-G
• rs1033069
• NM_024532.5:c.1215-29476A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024532.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPAG16	NM_024532.5	MANE Select	c.1215-29476A>G		intron	N/A	NP_078808.3
	SPAG16	NR_047659.2		n.1410-29476A>G		intron	N/A
	SPAG16	NR_047660.2		n.1116-29476A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPAG16	ENST00000331683.10	TSL:1 MANE Select	c.1215-29476A>G		intron	N/A	ENSP00000332592.5	Q8N0X2-1
	SPAG16	ENST00000406979.6	TSL:1	n.*1216-29476A>G		intron	N/A	ENSP00000385496.2	F8WB32
	SPAG16	ENST00000451561.1	TSL:3	c.272+37856A>G		intron	N/A	ENSP00000416600.1	H0Y811

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

African (AFR) AF: 0.356 AC: 14750 AN: 41464

American (AMR) AF: 0.618 AC: 9431 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1944 AN: 3464

East Asian (EAS) AF: 0.559 AC: 2887 AN: 5166

South Asian (SAS) AF: 0.839 AC: 4041 AN: 4814

European-Finnish (FIN) AF: 0.671 AC: 7087 AN: 10568

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.685 AC: 46530 AN: 67882

Other (OTH) AF: 0.567 AC: 1194 AN: 2104

Alfa AF: 0.671 Hom.: 17207

Bravo AF: 0.567

Asia WGS AF: 0.691 AC: 2403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.67
DANN	Benign	0.25
PhyloP100		-0.37
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1033069; hg19: chr2-214765208;