2-213852855-C-A

Variant names:

• chr2-213852855-C-A
• rs10498015
• NM_024532.5:c.1071-9630C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024532.5(SPAG16):​c.1071-9630C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 152,040 control chromosomes in the GnomAD database, including 9,674 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 0.35 (9674 hom., cov: 33)
• Consequence: SPAG16 NM_024532.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 6 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.435 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPAG16	NM_024532.5	MANE Select	c.1071-9630C>A		intron	N/A	NP_078808.3
	SPAG16	NR_047659.2		n.1266-9630C>A		intron	N/A
	SPAG16	NR_047660.2		n.972-9630C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPAG16	ENST00000331683.10	TSL:1 MANE Select	c.1071-9630C>A		intron	N/A	ENSP00000332592.5
	SPAG16	ENST00000406979.6	TSL:1	n.*1072-9630C>A		intron	N/A	ENSP00000385496.2
	SPAG16	ENST00000451561.1	TSL:3	c.129-9630C>A		intron	N/A	ENSP00000416600.1

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53379 AN: 151922 Hom.: 9677 Cov.: 33

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.351 AC: 53390 AN: 152040 Hom.: 9674 Cov.: 33 AF XY: 0.357 AC XY: 26521 AN XY: 74284

African (AFR) AF: 0.262 AC: 10865 AN: 41484

American (AMR) AF: 0.401 AC: 6122 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1086 AN: 3470

East Asian (EAS) AF: 0.448 AC: 2321 AN: 5176

South Asian (SAS) AF: 0.451 AC: 2173 AN: 4818

European-Finnish (FIN) AF: 0.393 AC: 4148 AN: 10548

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.373 AC: 25341 AN: 67966

Other (OTH) AF: 0.336 AC: 710 AN: 2112

Alfa AF: 0.362 Hom.: 32647

Bravo AF: 0.343

Asia WGS AF: 0.471 AC: 1639 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.50
DANN	Benign	0.39
PhyloP100		-1.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10498015; hg19: chr2-214717579;