rs10498015

Positions:

• chr2-213852855-C-A
• chr2-213852855-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.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

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPAG16	NM_024532.5	c.1071-9630C>A		intron_variant		ENST00000331683.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPAG16	ENST00000331683.10	c.1071-9630C>A		intron_variant		1	NM_024532.5	P1
SPAG16	ENST00000406979.6	c.*1072-9630C>A		intron_variant, NMD_transcript_variant		1
SPAG16	ENST00000451561.1	c.129-9630C>A		intron_variant		3
SPAG16	ENST00000452556.5	c.*637-9630C>A		intron_variant, NMD_transcript_variant		2

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

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.401

Gnomad4 ASJ AF: 0.313

Gnomad4 EAS AF: 0.448

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.393

Gnomad4 NFE AF: 0.373

Gnomad4 OTH AF: 0.336

Alfa AF: 0.366 Hom.: 21276

Bravo AF: 0.343

Asia WGS AF: 0.471 AC: 1639 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.50
DANN	Benign	0.39

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: rs10498015; hg19: chr2-214717579;