rs7607479

chr2-213678860-T-Cchr2-213678860-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024532.5(SPAG16):c.1071-183625T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 151,964 control chromosomes in the GnomAD database, including 13,921 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 0.41 (13921 hom., cov: 31)
• Consequence: SPAG16 NM_024532.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPAG16	NM_024532.5	c.1071-183625T>C		intron_variant		ENST00000331683.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPAG16	ENST00000331683.10	c.1071-183625T>C		intron_variant		1	NM_024532.5	P1
SPAG16	ENST00000406979.6	c.*1072-183625T>C		intron_variant, NMD_transcript_variant		1
SPAG16	ENST00000451561.1	c.129-183625T>C		intron_variant		3
SPAG16	ENST00000452556.5	c.*637-183625T>C		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62772 AN: 151846 Hom.: 13890 Cov.: 31

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.414 AC: 62848 AN: 151964 Hom.: 13921 Cov.: 31 AF XY: 0.406 AC XY: 30145 AN XY: 74290

Gnomad4 AFR AF: 0.564

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.476

Gnomad4 EAS AF: 0.357

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.367

Gnomad4 OTH AF: 0.443

Alfa AF: 0.376 Hom.: 5591

Bravo AF: 0.430

Asia WGS AF: 0.310 AC: 1079 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.076
Dann	Benign	0.34

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: rs7607479; hg19: chr2-214543584;