rs6756154

chr2-214100920-G-C

Variant summary

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

The NM_024532.5(SPAG16):c.1528-7276G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 151,850 control chromosomes in the GnomAD database, including 8,824 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 0.34 (8824 hom., cov: 32)
• Consequence: SPAG16 NM_024532.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.129

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]

LOC101928084 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPAG16	NM_024532.5	c.1528-7276G>C		intron_variant		ENST00000331683.10
LOC101928084	XR_241401.5	n.206+1278C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPAG16	ENST00000331683.10	c.1528-7276G>C		intron_variant		1	NM_024532.5	P1

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50902 AN: 151732 Hom.: 8811 Cov.: 32

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.336 AC: 50950 AN: 151850 Hom.: 8824 Cov.: 32 AF XY: 0.334 AC XY: 24779 AN XY: 74208

Gnomad4 AFR AF: 0.350

Gnomad4 AMR AF: 0.345

Gnomad4 ASJ AF: 0.308

Gnomad4 EAS AF: 0.196

Gnomad4 SAS AF: 0.254

Gnomad4 FIN AF: 0.347

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.321

Alfa AF: 0.344 Hom.: 1170

Bravo AF: 0.337

Asia WGS AF: 0.206 AC: 713 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.0
Dann	Benign	0.41

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: rs6756154; hg19: chr2-214965644;