rs10490502

Variant names:

• chr2-214244834-C-A
• rs10490502
• NM_024532.5:c.1720+95568C>A

Your query was ambiguous. Multiple possible variants found:

• chr2-214244834-C-A
• chr2-214244834-C-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.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
• Publications: 7 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]

ENSG00000197585 (HGNC:):

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPAG16	NM_024532.5	c.1720+95568C>A		intron_variant	Intron 15 of 15	ENST00000331683.10	NP_078808.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPAG16	ENST00000331683.10	c.1720+95568C>A		intron_variant	Intron 15 of 15	1	NM_024532.5	ENSP00000332592.5

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

African (AFR) AF: 0.153 AC: 6327 AN: 41436

American (AMR) AF: 0.110 AC: 1682 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 566 AN: 3470

East Asian (EAS) AF: 0.176 AC: 910 AN: 5164

South Asian (SAS) AF: 0.126 AC: 609 AN: 4820

European-Finnish (FIN) AF: 0.0940 AC: 990 AN: 10536

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 292

European-Non Finnish (NFE) AF: 0.0995 AC: 6761 AN: 67920

Other (OTH) AF: 0.128 AC: 270 AN: 2110

Alfa AF: 0.0939 Hom.: 442

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
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: rs10490502; hg19: chr2-215109558;