rs16851495

chr2-214108287-G-A

Variant summary

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

The NM_024532.5(SPAG16):c.1593+26G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0755 in 1,551,664 control chromosomes in the GnomAD database, including 5,883 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 (765 hom., cov: 32)
  • Exomes 𝑓: 0.074 (5118 hom.)
• Consequence: SPAG16 NM_024532.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.52

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=-0.98).
• 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	UniProt
SPAG16	NM_024532.5	c.1593+26G>A		intron_variant		ENST00000331683.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPAG16	ENST00000331683.10	c.1593+26G>A		intron_variant		1	NM_024532.5	P1

Frequencies

GnomAD3 genomes AF: 0.0876 AC: 13306 AN: 151906 Hom.: 764 Cov.: 32

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.0187

Gnomad AMR AF: 0.0706

Gnomad ASJ AF: 0.0784

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.0884

Gnomad FIN AF: 0.0655

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0644

Gnomad OTH AF: 0.0934

GnomAD3 exomes AF: 0.0892 AC: 21361 AN: 239522 Hom.: 1364 AF XY: 0.0870 AC XY: 11258 AN XY: 129418

Gnomad AFR exome AF: 0.115

Gnomad AMR exome AF: 0.0729

Gnomad ASJ exome AF: 0.0875

Gnomad EAS exome AF: 0.277

Gnomad SAS exome AF: 0.0778

Gnomad FIN exome AF: 0.0784

Gnomad NFE exome AF: 0.0653

Gnomad OTH exome AF: 0.0855

GnomAD4 exome AF: 0.0742 AC: 103870 AN: 1399640 Hom.: 5118 Cov.: 23 AF XY: 0.0743 AC XY: 51676 AN XY: 695934

Gnomad4 AFR exome AF: 0.116

Gnomad4 AMR exome AF: 0.0730

Gnomad4 ASJ exome AF: 0.0854

Gnomad4 EAS exome AF: 0.300

Gnomad4 SAS exome AF: 0.0790

Gnomad4 FIN exome AF: 0.0756

Gnomad4 NFE exome AF: 0.0632

Gnomad4 OTH exome AF: 0.0876

GnomAD4 genome AF: 0.0876 AC: 13316 AN: 152024 Hom.: 765 Cov.: 32 AF XY: 0.0884 AC XY: 6566 AN XY: 74294

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.0705

Gnomad4 ASJ AF: 0.0784

Gnomad4 EAS AF: 0.286

Gnomad4 SAS AF: 0.0879

Gnomad4 FIN AF: 0.0655

Gnomad4 NFE AF: 0.0644

Gnomad4 OTH AF: 0.0934

Alfa AF: 0.0732 Hom.: 111

Bravo AF: 0.0918

Asia WGS AF: 0.181 AC: 628 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.018
Dann	Benign	0.59

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: rs16851495; hg19: chr2-214973011; COSMIC: COSV59095599;