chr2-214144634-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.632
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

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
SPAG16NM_024532.5 linkc.1594-4506T>C intron_variant Intron 14 of 15 ENST00000331683.10 NP_078808.3 Q8N0X2-1Q4G1A2B4DYB5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SPAG16ENST00000331683.10 linkc.1594-4506T>C intron_variant Intron 14 of 15 1 NM_024532.5 ENSP00000332592.5 Q8N0X2-1

Frequencies

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7597126; hg19: chr2-215009358; API