2-214342920-C-T

Variant names:

• chr2-214342920-C-T
• rs10498009
• NM_024532.5:c.1721-67220C>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.1721-67220C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0645 in 152,046 control chromosomes in the GnomAD database, including 805 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 0.065 (805 hom., cov: 32)
• Consequence: SPAG16 NM_024532.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109
• Publications: 0 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]

ENSG00000197585 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.187 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.1721-67220C>T		intron	N/A	NP_078808.3
	SPAG16	NR_047659.2		n.1916-67220C>T		intron	N/A
	SPAG16	NR_047660.2		n.1622-67220C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPAG16	ENST00000331683.10	TSL:1 MANE Select	c.1721-67220C>T		intron	N/A	ENSP00000332592.5	Q8N0X2-1
	SPAG16	ENST00000406979.6	TSL:1	n.*1722-67220C>T		intron	N/A	ENSP00000385496.2	F8WB32
	SPAG16	ENST00000451561.1	TSL:3	c.593-67220C>T		intron	N/A	ENSP00000416600.1	H0Y811

Frequencies

GnomAD3 genomes AF: 0.0643 AC: 9775 AN: 151928 Hom.: 799 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0347

Gnomad ASJ AF: 0.00288

Gnomad EAS AF: 0.0247

Gnomad SAS AF: 0.00374

Gnomad FIN AF: 0.0138

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0138

Gnomad OTH AF: 0.0569

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

GnomAD4 genome AF: 0.0645 AC: 9809 AN: 152046 Hom.: 805 Cov.: 32 AF XY: 0.0631 AC XY: 4690 AN XY: 74344

African (AFR) AF: 0.191 AC: 7905 AN: 41422

American (AMR) AF: 0.0346 AC: 529 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.00288 AC: 10 AN: 3468

East Asian (EAS) AF: 0.0245 AC: 127 AN: 5176

South Asian (SAS) AF: 0.00354 AC: 17 AN: 4808

European-Finnish (FIN) AF: 0.0138 AC: 146 AN: 10582

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0138 AC: 938 AN: 67984

Other (OTH) AF: 0.0563 AC: 119 AN: 2114

Alfa AF: 0.0306 Hom.: 86

Bravo AF: 0.0734

Asia WGS AF: 0.0270 AC: 94 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.5
DANN	Benign	0.56
PhyloP100		-0.11
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: rs10498009; hg19: chr2-215207644;