Variant X-38073633-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_138780.3(SYTL5):c.489A>G(p.Ala163=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 1,195,168 control chromosomes in the GnomAD database, including 27,479 homozygotes. There are 97,531 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.29 ( 3865 hom., 9223 hem., cov: 22)

Exomes 𝑓: 0.25 ( 23614 hom. 88308 hem. )

Consequence

SYTL5
NM_138780.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.198

Variant links:

Genes affected

SYTL5 (HGNC:15589): (synaptotagmin like 5) The protein encoded by this gene belongs to the synaptotagmin-like (Slp) protein family, which contains a unique homology domain at the N-terminus, referred to as the Slp homology domain (SHD). The SHD functions as a binding site for Rab27A, which plays a role in protein transport. Expression of this gene is restricted to placenta and liver, suggesting that it might be involved in Rab27A-dependent membrane trafficking in specific tissues. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]

SYTL5 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=-0.92).

BP6

Variant X-38073633-A-G is Benign according to our data. Variant chrX-38073633-A-G is described in Lovd as [Likely_benign].

BP7

Synonymous conserved (PhyloP=-0.198 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SYTL5	NM_138780.3 linkuse as main transcript	c.489A>G	p.Ala163=	synonymous_variant	5/17	ENST00000297875.7	NP_620135.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SYTL5	ENST00000297875.7 linkuse as main transcript	c.489A>G	p.Ala163=	synonymous_variant	5/17	5	NM_138780.3	ENSP00000297875	P4	Q8TDW5-1
SYTL5	ENST00000456733.2 linkuse as main transcript	c.489A>G	p.Ala163=	synonymous_variant	4/17	1		ENSP00000395220	A1	Q8TDW5-2

Frequencies

GnomAD3 genomes

AF:

0.292

AC:

32276

AN:

110620

Hom.:

3865

Cov.:

AF XY:

0.280

AC XY:

9199

AN XY:

32910

show subpopulations

Gnomad AFR

AF:

0.416

Gnomad AMI

AF:

0.214

Gnomad AMR

AF:

0.345

Gnomad ASJ

AF:

0.235

Gnomad EAS

AF:

0.0951

Gnomad SAS

AF:

0.368

Gnomad FIN

AF:

0.123

Gnomad MID

AF:

0.310

Gnomad NFE

AF:

0.242

Gnomad OTH

AF:

0.311

GnomAD3 exomes

AF:

0.245

AC:

38576

AN:

157759

Hom.:

4034

AF XY:

0.222

AC XY:

10829

AN XY:

48779

show subpopulations

Gnomad AFR exome

AF:

0.412

Gnomad AMR exome

AF:

0.335

Gnomad ASJ exome

AF:

0.218

Gnomad EAS exome

AF:

0.0939

Gnomad SAS exome

AF:

0.347

Gnomad FIN exome

AF:

0.127

Gnomad NFE exome

AF:

0.217

Gnomad OTH exome

AF:

0.265

GnomAD4 exome

AF:

0.248

AC:

269093

AN:

1084491

Hom.:

23614

Cov.:

AF XY:

0.249

AC XY:

88308

AN XY:

354113

show subpopulations

Gnomad4 AFR exome

AF:

0.436

Gnomad4 AMR exome

AF:

0.338

Gnomad4 ASJ exome

AF:

0.222

Gnomad4 EAS exome

AF:

0.109

Gnomad4 SAS exome

AF:

0.351

Gnomad4 FIN exome

AF:

0.139

Gnomad4 NFE exome

AF:

0.242

Gnomad4 OTH exome

AF:

0.269

GnomAD4 genome

AF:

0.292

AC:

32294

AN:

110677

Hom.:

3865

Cov.:

AF XY:

0.280

AC XY:

9223

AN XY:

32977

show subpopulations

Gnomad4 AFR

AF:

0.416

Gnomad4 AMR

AF:

0.345

Gnomad4 ASJ

AF:

0.235

Gnomad4 EAS

AF:

0.0945

Gnomad4 SAS

AF:

0.368

Gnomad4 FIN

AF:

0.123

Gnomad4 NFE

AF:

0.242

Gnomad4 OTH

AF:

0.307

Alfa

AF:

0.268

Hom.:

4807

Bravo

AF:

0.316

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.1

DANN

Benign

0.48

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over