Variant 2-213862481-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_024532.5(SPAG16):c.1071-4G>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00546 in 1,612,676 control chromosomes in the GnomAD database, including 404 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.028 ( 211 hom., cov: 33)

Exomes 𝑓: 0.0031 ( 193 hom. )

Consequence

SPAG16
NM_024532.5 splice_region, splice_polypyrimidine_tract, intron

Scores

Splicing: ADA: 0.00005070

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.789

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]

SPAG16 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 2-213862481-G-T is Benign according to our data. Variant chr2-213862481-G-T is described in ClinVar as [Benign]. Clinvar id is 767850.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0935 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPAG16	NM_024532.5 linkuse as main transcript	c.1071-4G>T		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000331683.10

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
SPAG16	ENST00000331683.10 linkuse as main transcript	c.1071-4G>T	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant	1	NM_024532.5	P1	Q8N0X2-1
SPAG16	ENST00000406979.6 linkuse as main transcript	c.*1072-4G>T	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant	1
SPAG16	ENST00000451561.1 linkuse as main transcript	c.129-4G>T	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant	3
SPAG16	ENST00000452556.5 linkuse as main transcript	c.*637-4G>T	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant	2

Frequencies

GnomAD3 genomes

AF:

0.0276

AC:

4199

AN:

151912

Hom.:

209

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0960

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00852

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000568

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.000662

Gnomad OTH

AF:

0.0230

GnomAD3 exomes

AF:

0.00766

AC:

1920

AN:

250640

Hom.:

AF XY:

0.00552

AC XY:

748

AN XY:

135410

show subpopulations

Gnomad AFR exome

AF:

0.0997

Gnomad AMR exome

AF:

0.00516

Gnomad ASJ exome

AF:

0.000498

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000196

Gnomad FIN exome

AF:

0.000694

Gnomad NFE exome

AF:

0.000557

Gnomad OTH exome

AF:

0.00540

GnomAD4 exome

AF:

0.00314

AC:

4589

AN:

1460646

Hom.:

193

Cov.:

AF XY:

0.00277

AC XY:

2011

AN XY:

726492

show subpopulations

Gnomad4 AFR exome

AF:

0.101

Gnomad4 AMR exome

AF:

0.00548

Gnomad4 ASJ exome

AF:

0.000345

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000209

Gnomad4 FIN exome

AF:

0.000618

Gnomad4 NFE exome

AF:

0.000340

Gnomad4 OTH exome

AF:

0.00772

GnomAD4 genome

AF:

0.0277

AC:

4211

AN:

152030

Hom.:

211

Cov.:

AF XY:

0.0268

AC XY:

1994

AN XY:

74300

show subpopulations

Gnomad4 AFR

AF:

0.0960

Gnomad4 AMR

AF:

0.00851

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000568

Gnomad4 NFE

AF:

0.000662

Gnomad4 OTH

AF:

0.0227

Alfa

AF:

0.00819

Hom.:

Bravo

AF:

0.0318

Asia WGS

AF:

0.0120

AC:

AN:

3478

EpiCase

AF:

0.000656

EpiControl

AF:

0.000832

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Aug 15, 2017

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.29

DANN

Benign

0.38

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000051

dbscSNV1_RF

Benign

0.016

SpliceAI score (max)

0.050

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over