chr2-213691803-G-T

Variant names:

• chr2-213691803-G-T
• rs4132244
• NM_024532.5:c.1071-170682G>T

Variant summary

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

The NM_024532.5(SPAG16):​c.1071-170682G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 152,058 control chromosomes in the GnomAD database, including 7,770 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 0.31 (7770 hom., cov: 32)
• Consequence: SPAG16 NM_024532.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.390
• Publications: 2 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.346 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.1071-170682G>T		intron	N/A	NP_078808.3
	SPAG16	NR_047659.2		n.1266-170682G>T		intron	N/A
	SPAG16	NR_047660.2		n.972-170682G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPAG16	ENST00000331683.10	TSL:1 MANE Select	c.1071-170682G>T		intron	N/A	ENSP00000332592.5	Q8N0X2-1
	SPAG16	ENST00000406979.6	TSL:1	n.*1072-170682G>T		intron	N/A	ENSP00000385496.2	F8WB32
	SPAG16	ENST00000451561.1	TSL:3	c.129-170682G>T		intron	N/A	ENSP00000416600.1	H0Y811

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47723 AN: 151940 Hom.: 7759 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.314 AC: 47767 AN: 152058 Hom.: 7770 Cov.: 32 AF XY: 0.309 AC XY: 22994 AN XY: 74338

African (AFR) AF: 0.274 AC: 11372 AN: 41460

American (AMR) AF: 0.302 AC: 4610 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1318 AN: 3468

East Asian (EAS) AF: 0.312 AC: 1613 AN: 5176

South Asian (SAS) AF: 0.256 AC: 1233 AN: 4820

European-Finnish (FIN) AF: 0.265 AC: 2797 AN: 10566

Middle Eastern (MID) AF: 0.421 AC: 123 AN: 292

European-Non Finnish (NFE) AF: 0.350 AC: 23797 AN: 67970

Other (OTH) AF: 0.353 AC: 746 AN: 2114

Alfa AF: 0.335 Hom.: 36084

Bravo AF: 0.318

Asia WGS AF: 0.240 AC: 835 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.6
DANN	Benign	0.55
PhyloP100		0.39
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: rs4132244; hg19: chr2-214556527;