rs16851771

chr2-214323895-A-G

Variant summary

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

The NM_024532.5(SPAG16):c.1721-86245A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0918 in 152,274 control chromosomes in the GnomAD database, including 817 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 0.092 (817 hom., cov: 33)
• Consequence: SPAG16 NM_024532.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.238

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) 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.1721-86245A>G		intron_variant		ENST00000331683.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPAG16	ENST00000331683.10	c.1721-86245A>G		intron_variant		1	NM_024532.5	P1
	ENST00000412896.5	n.304-73717T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0916 AC: 13937 AN: 152156 Hom.: 811 Cov.: 33

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.0696

Gnomad ASJ AF: 0.0193

Gnomad EAS AF: 0.0269

Gnomad SAS AF: 0.0192

Gnomad FIN AF: 0.0409

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0707

Gnomad OTH AF: 0.0832

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

GnomAD4 genome AF: 0.0918 AC: 13977 AN: 152274 Hom.: 817 Cov.: 33 AF XY: 0.0883 AC XY: 6577 AN XY: 74458

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.0696

Gnomad4 ASJ AF: 0.0193

Gnomad4 EAS AF: 0.0268

Gnomad4 SAS AF: 0.0192

Gnomad4 FIN AF: 0.0409

Gnomad4 NFE AF: 0.0707

Gnomad4 OTH AF: 0.0823

Alfa AF: 0.0730 Hom.: 321

Bravo AF: 0.0989

Asia WGS AF: 0.0350 AC: 121 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	3.9
Dann	Benign	0.67

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: rs16851771; hg19: chr2-215188619;