rs10490495

Positions:

• chr2-214102297-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024532.5(SPAG16):​c.1528-5899G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0884 in 151,954 control chromosomes in the GnomAD database, including 771 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 0.088 (771 hom., cov: 30)
• Consequence: SPAG16 NM_024532.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.127

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]

LOC101928084 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SPAG16	NM_024532.5	c.1528-5899G>T		intron_variant		ENST00000331683.10	NP_078808.3
LOC101928084	XR_241401.5	n.124-17C>A		splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPAG16	ENST00000331683.10	c.1528-5899G>T		intron_variant		1	NM_024532.5	ENSP00000332592	P1

Frequencies

GnomAD3 genomes AF: 0.0884 AC: 13419 AN: 151834 Hom.: 770 Cov.: 30

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.0187

Gnomad AMR AF: 0.0713

Gnomad ASJ AF: 0.0781

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.0877

Gnomad FIN AF: 0.0651

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0646

Gnomad OTH AF: 0.0964

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

GnomAD4 genome AF: 0.0884 AC: 13431 AN: 151954 Hom.: 771 Cov.: 30 AF XY: 0.0891 AC XY: 6622 AN XY: 74288

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.0712

Gnomad4 ASJ AF: 0.0781

Gnomad4 EAS AF: 0.285

Gnomad4 SAS AF: 0.0871

Gnomad4 FIN AF: 0.0651

Gnomad4 NFE AF: 0.0646

Gnomad4 OTH AF: 0.0964

Alfa AF: 0.0706 Hom.: 60

Bravo AF: 0.0932

Asia WGS AF: 0.181 AC: 627 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.58
DANN	Benign	0.55

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: rs10490495; hg19: chr2-214967021;