rs16850268

Variant names:

• chr2-213396532-A-G
• rs16850268
• NM_024532.5:c.942+21413A>G

Variant summary

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

The NM_024532.5(SPAG16):​c.942+21413A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0647 in 316,166 control chromosomes in the GnomAD database, including 2,242 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 0.099 (1947 hom., cov: 32)
  • Exomes 𝑓: 0.033 (295 hom.)
• Consequence: SPAG16 NM_024532.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.165
• Publications: 1 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024532.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPAG16	NM_024532.5	MANE Select	c.942+21413A>G		intron	N/A	NP_078808.3
	SPAG16	NR_047659.2		n.1137+21413A>G		intron	N/A
	SPAG16	NR_047660.2		n.843+21413A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPAG16	ENST00000331683.10	TSL:1 MANE Select	c.942+21413A>G		intron	N/A	ENSP00000332592.5	Q8N0X2-1
	SPAG16	ENST00000447990.1	TSL:1	c.942+21413A>G		intron	N/A	ENSP00000400847.1	E7EWV3
	SPAG16	ENST00000406979.6	TSL:1	n.*943+21413A>G		intron	N/A	ENSP00000385496.2	F8WB32

Frequencies

GnomAD3 genomes AF: 0.0987 AC: 15020 AN: 152112 Hom.: 1937 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0487

Gnomad ASJ AF: 0.0608

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0373

Gnomad FIN AF: 0.0160

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0180

Gnomad OTH AF: 0.0819

GnomAD4 exome AF: 0.0330 AC: 5404 AN: 163938 Hom.: 295 AF XY: 0.0329 AC XY: 3064 AN XY: 93052

African (AFR) AF: 0.306 AC: 1317 AN: 4306

American (AMR) AF: 0.0269 AC: 325 AN: 12098

Ashkenazi Jewish (ASJ) AF: 0.0659 AC: 352 AN: 5338

East Asian (EAS) AF: 0.00120 AC: 7 AN: 5846

South Asian (SAS) AF: 0.0412 AC: 1343 AN: 32574

European-Finnish (FIN) AF: 0.0144 AC: 121 AN: 8426

Middle Eastern (MID) AF: 0.0517 AC: 116 AN: 2242

European-Non Finnish (NFE) AF: 0.0176 AC: 1497 AN: 85128

Other (OTH) AF: 0.0409 AC: 326 AN: 7980

GnomAD4 genome AF: 0.0990 AC: 15064 AN: 152228 Hom.: 1947 Cov.: 32 AF XY: 0.0956 AC XY: 7116 AN XY: 74440

African (AFR) AF: 0.297 AC: 12344 AN: 41508

American (AMR) AF: 0.0485 AC: 742 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0608 AC: 211 AN: 3470

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5184

South Asian (SAS) AF: 0.0373 AC: 180 AN: 4820

European-Finnish (FIN) AF: 0.0160 AC: 170 AN: 10620

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0180 AC: 1225 AN: 68022

Other (OTH) AF: 0.0810 AC: 171 AN: 2110

Alfa AF: 0.157 Hom.: 771

Bravo AF: 0.111

Asia WGS AF: 0.0570 AC: 200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.3
DANN	Benign	0.78
PhyloP100		0.17
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: rs16850268; hg19: chr2-214261256;