chr2-213973789-G-T

Variant names:

• chr2-213973789-G-T
• rs9789347
• NM_024532.5:c.1401-40162G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024532.5(SPAG16):​c.1401-40162G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 151,828 control chromosomes in the GnomAD database, including 3,965 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 0.21 (3965 hom., cov: 31)
• Consequence: SPAG16 NM_024532.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0490
• Publications: 6 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPAG16	NM_024532.5	c.1401-40162G>T		intron_variant	Intron 12 of 15	ENST00000331683.10	NP_078808.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPAG16	ENST00000331683.10	c.1401-40162G>T		intron_variant	Intron 12 of 15	1	NM_024532.5	ENSP00000332592.5

Frequencies

GnomAD3 genomes AF: 0.211 AC: 31999 AN: 151708 Hom.: 3963 Cov.: 31

Gnomad AFR AF: 0.0899

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.211 AC: 32004 AN: 151828 Hom.: 3965 Cov.: 31 AF XY: 0.216 AC XY: 15994 AN XY: 74174

African (AFR) AF: 0.0898 AC: 3724 AN: 41454

American (AMR) AF: 0.276 AC: 4200 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 758 AN: 3466

East Asian (EAS) AF: 0.357 AC: 1841 AN: 5152

South Asian (SAS) AF: 0.413 AC: 1983 AN: 4800

European-Finnish (FIN) AF: 0.205 AC: 2161 AN: 10542

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16459 AN: 67906

Other (OTH) AF: 0.208 AC: 437 AN: 2102

Alfa AF: 0.230 Hom.: 11789

Bravo AF: 0.205

Asia WGS AF: 0.412 AC: 1431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.0
DANN	Benign	0.44
PhyloP100		0.049
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: rs9789347; hg19: chr2-214838513;