2-214052678-A-C

Variant names:

• chr2-214052678-A-C
• rs1510552
• NM_024532.5:c.1527+38601A>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.1527+38601A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.803 in 152,114 control chromosomes in the GnomAD database, including 49,493 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 0.80 (49493 hom., cov: 32)
• Consequence: SPAG16 NM_024532.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.96
• Publications: 4 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=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.875 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPAG16	NM_024532.5	MANE Select	c.1527+38601A>C		intron	N/A	NP_078808.3
	SPAG16	NR_047659.2		n.1722+38601A>C		intron	N/A
	SPAG16	NR_047660.2		n.1428+38601A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPAG16	ENST00000331683.10	TSL:1 MANE Select	c.1527+38601A>C		intron	N/A	ENSP00000332592.5
	SPAG16	ENST00000406979.6	TSL:1	n.*1528+38601A>C		intron	N/A	ENSP00000385496.2
	SPAG16	ENST00000451561.1	TSL:3	c.399+38601A>C		intron	N/A	ENSP00000416600.1

Frequencies

GnomAD3 genomes AF: 0.803 AC: 122063 AN: 151994 Hom.: 49451 Cov.: 32

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.851

Gnomad AMR AF: 0.839

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.799

Gnomad SAS AF: 0.898

Gnomad FIN AF: 0.881

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.844

Gnomad OTH AF: 0.792

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

GnomAD4 genome AF: 0.803 AC: 122162 AN: 152114 Hom.: 49493 Cov.: 32 AF XY: 0.807 AC XY: 60015 AN XY: 74362

African (AFR) AF: 0.690 AC: 28612 AN: 41472

American (AMR) AF: 0.840 AC: 12825 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.817 AC: 2838 AN: 3472

East Asian (EAS) AF: 0.799 AC: 4136 AN: 5174

South Asian (SAS) AF: 0.898 AC: 4322 AN: 4814

European-Finnish (FIN) AF: 0.881 AC: 9334 AN: 10590

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.844 AC: 57401 AN: 68004

Other (OTH) AF: 0.794 AC: 1672 AN: 2106

Alfa AF: 0.827 Hom.: 196884

Bravo AF: 0.791

Asia WGS AF: 0.882 AC: 3067 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.016
DANN	Benign	0.45
PhyloP100		-3.0
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: rs1510552; hg19: chr2-214917402;