rs10498008

Variant names:

• chr2-213480791-G-A
• rs10498008
• NM_024532.5:c.943-9172G>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.943-9172G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0963 in 152,202 control chromosomes in the GnomAD database, including 1,840 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 0.096 (1840 hom., cov: 33)
• Consequence: SPAG16 NM_024532.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.385

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPAG16	NM_024532.5	c.943-9172G>A		intron_variant	Intron 9 of 15	ENST00000331683.10	NP_078808.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPAG16	ENST00000331683.10	c.943-9172G>A		intron_variant	Intron 9 of 15	1	NM_024532.5	ENSP00000332592.5
SPAG16	ENST00000406979.6	n.*944-9172G>A		intron_variant	Intron 11 of 17	1		ENSP00000385496.2
SPAG16	ENST00000452556.5	n.*509-9172G>A		intron_variant	Intron 7 of 13	2		ENSP00000398926.1

Frequencies

GnomAD3 genomes AF: 0.0961 AC: 14617 AN: 152084 Hom.: 1833 Cov.: 33

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0479

Gnomad ASJ AF: 0.0608

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0381

Gnomad FIN AF: 0.0161

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0180

Gnomad OTH AF: 0.0826

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

GnomAD4 genome AF: 0.0963 AC: 14657 AN: 152202 Hom.: 1840 Cov.: 33 AF XY: 0.0931 AC XY: 6927 AN XY: 74414

Gnomad4 AFR AF: 0.288 AC: 0.287725 AN: 0.287725

Gnomad4 AMR AF: 0.0477 AC: 0.0477436 AN: 0.0477436

Gnomad4 ASJ AF: 0.0608 AC: 0.0607719 AN: 0.0607719

Gnomad4 EAS AF: 0.00135 AC: 0.00134875 AN: 0.00134875

Gnomad4 SAS AF: 0.0384 AC: 0.0383658 AN: 0.0383658

Gnomad4 FIN AF: 0.0161 AC: 0.0161199 AN: 0.0161199

Gnomad4 NFE AF: 0.0180 AC: 0.0180294 AN: 0.0180294

Gnomad4 OTH AF: 0.0818 AC: 0.081758 AN: 0.081758

Alfa AF: 0.0615 Hom.: 133

Bravo AF: 0.108

Asia WGS AF: 0.0550 AC: 193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.0
DANN	Benign	0.69
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

Publications

LitVar

Other links and lift over

dbSNP: rs10498008; hg19: chr2-214345515;