chr2-213862643-C-G

Variant names:

• chr2-213862643-C-G
• rs2042792
• NM_024532.5:c.1214+15C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024532.5(SPAG16):​c.1214+15C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 1,612,300 control chromosomes in the GnomAD database, including 117,429 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 (9405 hom., cov: 31)
  • Exomes 𝑓: 0.38 (108024 hom.)
• Consequence: SPAG16 NM_024532.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.462
• Publications: 7 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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPAG16	NM_024532.5	c.1214+15C>G		intron_variant	Intron 11 of 15	ENST00000331683.10	NP_078808.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPAG16	ENST00000331683.10	c.1214+15C>G		intron_variant	Intron 11 of 15	1	NM_024532.5	ENSP00000332592.5
SPAG16	ENST00000406979.6	n.*1215+15C>G		intron_variant	Intron 13 of 17	1		ENSP00000385496.2
SPAG16	ENST00000451561.1	c.272+15C>G		intron_variant	Intron 2 of 5	3		ENSP00000416600.1
SPAG16	ENST00000452556.5	n.*780+15C>G		intron_variant	Intron 9 of 13	2		ENSP00000398926.1

Frequencies

GnomAD3 genomes AF: 0.343 AC: 52087 AN: 151802 Hom.: 9406 Cov.: 31

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.331

GnomAD2 exomes AF: 0.389 AC: 97397 AN: 250494 AF XY: 0.392

Gnomad AFR exome AF: 0.225

Gnomad AMR exome AF: 0.431

Gnomad ASJ exome AF: 0.307

Gnomad EAS exome AF: 0.430

Gnomad FIN exome AF: 0.394

Gnomad NFE exome AF: 0.380

Gnomad OTH exome AF: 0.368

GnomAD4 exome AF: 0.381 AC: 556862 AN: 1460382 Hom.: 108024 Cov.: 34 AF XY: 0.384 AC XY: 278774 AN XY: 726462

African (AFR) AF: 0.217 AC: 7263 AN: 33458

American (AMR) AF: 0.425 AC: 18993 AN: 44660

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 7911 AN: 26104

East Asian (EAS) AF: 0.488 AC: 19349 AN: 39674

South Asian (SAS) AF: 0.459 AC: 39565 AN: 86214

European-Finnish (FIN) AF: 0.399 AC: 21252 AN: 53328

Middle Eastern (MID) AF: 0.340 AC: 1943 AN: 5720

European-Non Finnish (NFE) AF: 0.377 AC: 418511 AN: 1110886

Other (OTH) AF: 0.366 AC: 22075 AN: 60338

GnomAD4 genome AF: 0.343 AC: 52103 AN: 151918 Hom.: 9405 Cov.: 31 AF XY: 0.349 AC XY: 25933 AN XY: 74222

African (AFR) AF: 0.229 AC: 9492 AN: 41438

American (AMR) AF: 0.400 AC: 6103 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1070 AN: 3464

East Asian (EAS) AF: 0.452 AC: 2322 AN: 5138

South Asian (SAS) AF: 0.472 AC: 2274 AN: 4814

European-Finnish (FIN) AF: 0.393 AC: 4141 AN: 10530

Middle Eastern (MID) AF: 0.288 AC: 84 AN: 292

European-Non Finnish (NFE) AF: 0.373 AC: 25382 AN: 67958

Other (OTH) AF: 0.332 AC: 699 AN: 2104

Alfa AF: 0.348 Hom.: 1708

Bravo AF: 0.334

Asia WGS AF: 0.476 AC: 1659 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.63
DANN	Benign	0.36
PhyloP100		-0.46
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: rs2042792; hg19: chr2-214727367; COSMIC: COSV59079150;