rs6707387

Positions:

• chr2-213683813-G-A
• chr2-213683813-G-C
• chr2-213683813-G-T

Variant summary

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

The NM_024532.5(SPAG16):​c.1071-178672G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152,020 control chromosomes in the GnomAD database, including 4,146 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 0.21 (4146 hom., cov: 32)
• Consequence: SPAG16 NM_024532.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SPAG16	NM_024532.5	c.1071-178672G>A		intron_variant		ENST00000331683.10	NP_078808.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPAG16	ENST00000331683.10	c.1071-178672G>A		intron_variant		1	NM_024532.5	ENSP00000332592	P1
SPAG16	ENST00000406979.6	c.*1072-178672G>A		intron_variant, NMD_transcript_variant		1		ENSP00000385496
SPAG16	ENST00000451561.1	c.129-178672G>A		intron_variant		3		ENSP00000416600
SPAG16	ENST00000452556.5	c.*637-178672G>A		intron_variant, NMD_transcript_variant		2		ENSP00000398926

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31794 AN: 151902 Hom.: 4147 Cov.: 32

Gnomad AFR AF: 0.0618

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.209 AC: 31789 AN: 152020 Hom.: 4146 Cov.: 32 AF XY: 0.208 AC XY: 15417 AN XY: 74296

Gnomad4 AFR AF: 0.0616

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.320

Gnomad4 EAS AF: 0.355

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.248

Alfa AF: 0.195 Hom.: 949

Bravo AF: 0.206

Asia WGS AF: 0.218 AC: 754 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.062
DANN	Benign	0.37

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: rs6707387; hg19: chr2-214548537;