rs10490502

Positions:

• chr2-214244834-C-A
• chr2-214244834-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+95568C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 151,898 control chromosomes in the GnomAD database, including 1,143 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 0.12 (1143 hom., cov: 32)
• 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]

LOC124907973 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPAG16	NM_024532.5	c.1720+95568C>A		intron_variant		ENST00000331683.10
LOC124907973	XR_007088072.1	n.491+1196G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPAG16	ENST00000331683.10	c.1720+95568C>A		intron_variant		1	NM_024532.5	P1

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18200 AN: 151780 Hom.: 1137 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.0945

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.0940

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0995

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.120 AC: 18235 AN: 151898 Hom.: 1143 Cov.: 32 AF XY: 0.121 AC XY: 8946 AN XY: 74222

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.0940

Gnomad4 NFE AF: 0.0995

Gnomad4 OTH AF: 0.128

Alfa AF: 0.0933 Hom.: 395

Bravo AF: 0.125

Asia WGS AF: 0.184 AC: 642 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.16
DANN	Benign	0.53

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: rs10490502; hg19: chr2-215109558;