2-213520188-C-G

Variant names:

• chr2-213520188-C-G
• rs10932486
• NM_024532.5:c.1070+30098C>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_024532.5(SPAG16):​c.1070+30098C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 151,886 control chromosomes in the GnomAD database, including 6,352 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 0.27 (6352 hom., cov: 30)
• Consequence: SPAG16 NM_024532.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220
• Publications: 2 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPAG16	NM_024532.5	c.1070+30098C>G		intron_variant	Intron 10 of 15	ENST00000331683.10	NP_078808.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPAG16	ENST00000331683.10	c.1070+30098C>G		intron_variant	Intron 10 of 15	1	NM_024532.5	ENSP00000332592.5
SPAG16	ENST00000406979.6	n.*1071+30098C>G		intron_variant	Intron 12 of 17	1		ENSP00000385496.2
SPAG16	ENST00000451561.1	c.128+30098C>G		intron_variant	Intron 1 of 5	3		ENSP00000416600.1
SPAG16	ENST00000452556.5	n.*636+30098C>G		intron_variant	Intron 8 of 13	2		ENSP00000398926.1

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40761 AN: 151768 Hom.: 6353 Cov.: 30

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.268 AC: 40762 AN: 151886 Hom.: 6352 Cov.: 30 AF XY: 0.265 AC XY: 19638 AN XY: 74208

African (AFR) AF: 0.116 AC: 4821 AN: 41474

American (AMR) AF: 0.289 AC: 4412 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1189 AN: 3464

East Asian (EAS) AF: 0.329 AC: 1693 AN: 5148

South Asian (SAS) AF: 0.250 AC: 1198 AN: 4786

European-Finnish (FIN) AF: 0.261 AC: 2754 AN: 10536

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.350 AC: 23783 AN: 67912

Other (OTH) AF: 0.310 AC: 652 AN: 2102

Alfa AF: 0.302 Hom.: 968

Bravo AF: 0.267

Asia WGS AF: 0.231 AC: 802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	7.4
DANN	Benign	0.81
PhyloP100		0.22
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: rs10932486; hg19: chr2-214384912;