chr2-214144634-T-C

Variant names:

• chr2-214144634-T-C
• rs7597126
• NM_024532.5:c.1594-4506T>C

Variant summary

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

The NM_024532.5(SPAG16):​c.1594-4506T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 151,946 control chromosomes in the GnomAD database, including 13,404 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 0.39 (13404 hom., cov: 32)
• Consequence: SPAG16 NM_024532.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.632

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.504 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPAG16	NM_024532.5	c.1594-4506T>C		intron_variant	Intron 14 of 15	ENST00000331683.10	NP_078808.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPAG16	ENST00000331683.10	c.1594-4506T>C		intron_variant	Intron 14 of 15	1	NM_024532.5	ENSP00000332592.5

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59249 AN: 151828 Hom.: 13408 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.390 AC: 59249 AN: 151946 Hom.: 13404 Cov.: 32 AF XY: 0.391 AC XY: 29013 AN XY: 74252

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.353

Gnomad4 FIN AF: 0.591

Gnomad4 NFE AF: 0.508

Gnomad4 OTH AF: 0.394

Alfa AF: 0.458 Hom.: 6917

Bravo AF: 0.362

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.51
DANN	Benign	0.78

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: rs7597126; hg19: chr2-215009358;