chr2-213520188-C-G

Position:

• chr2-213520188-C-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000331683.10(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 ENST00000331683.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220

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 -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/exons	MANE	Protein	UniProt
SPAG16	NM_024532.5	c.1070+30098C>G		intron_variant		ENST00000331683.10	NP_078808.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPAG16	ENST00000331683.10	c.1070+30098C>G		intron_variant		1	NM_024532.5	ENSP00000332592	P1
SPAG16	ENST00000406979.6	c.*1071+30098C>G		intron_variant, NMD_transcript_variant		1		ENSP00000385496
SPAG16	ENST00000451561.1	c.128+30098C>G		intron_variant		3		ENSP00000416600
SPAG16	ENST00000452556.5	c.*636+30098C>G		intron_variant, NMD_transcript_variant		2		ENSP00000398926

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

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.350

Gnomad4 OTH AF: 0.310

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

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: rs10932486; hg19: chr2-214384912;