2-213678860-T-C

Variant names:

• chr2-213678860-T-C
• rs7607479
• NM_024532.5:c.1071-183625T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 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]

ACMG classification

Our verdict: Benign. The variant received -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.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPAG16	NM_024532.5	MANE Select	c.1071-183625T>C		intron	N/A	NP_078808.3
	SPAG16	NR_047659.2		n.1266-183625T>C		intron	N/A
	SPAG16	NR_047660.2		n.972-183625T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPAG16	ENST00000331683.10	TSL:1 MANE Select	c.1071-183625T>C		intron	N/A	ENSP00000332592.5
	SPAG16	ENST00000406979.6	TSL:1	n.*1072-183625T>C		intron	N/A	ENSP00000385496.2
	SPAG16	ENST00000451561.1	TSL:3	c.129-183625T>C		intron	N/A	ENSP00000416600.1

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

African (AFR) AF: 0.564 AC: 23385 AN: 41446

American (AMR) AF: 0.356 AC: 5433 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.476 AC: 1652 AN: 3470

East Asian (EAS) AF: 0.357 AC: 1837 AN: 5144

South Asian (SAS) AF: 0.303 AC: 1458 AN: 4816

European-Finnish (FIN) AF: 0.276 AC: 2923 AN: 10580

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.367 AC: 24936 AN: 67944

Other (OTH) AF: 0.443 AC: 933 AN: 2108

Alfa AF: 0.376 Hom.: 6187

Bravo AF: 0.430

Asia WGS AF: 0.310 AC: 1079 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.076
DANN	Benign	0.34
PhyloP100		-2.1
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: rs7607479; hg19: chr2-214543584;