Variant X-38108615-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_138780.3(SYTL5):c.1350T>C(p.Tyr450=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 1,185,999 control chromosomes in the GnomAD database, including 36,927 homozygotes. There are 101,193 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 0.39 ( 8631 hom., 12203 hem., cov: 22)

Exomes 𝑓: 0.26 ( 28296 hom. 88990 hem. )

Consequence

SYTL5
NM_138780.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.288

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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.56).

BP6

Variant X-38108615-T-C is Benign according to our data. Variant chrX-38108615-T-C is described in Lovd as [Likely_benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.761 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.1350T>C	p.Tyr450=	synonymous_variant	12/17	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.1350T>C	p.Tyr450=	synonymous_variant	12/17	5	NM_138780.3	ENSP00000297875	P4	Q8TDW5-1
SYTL5	ENST00000456733.2 linkuse as main transcript	c.1416T>C	p.Tyr472=	synonymous_variant	12/17	1		ENSP00000395220	A1	Q8TDW5-2

Frequencies

GnomAD3 genomes

AF:

0.392

AC:

43370

AN:

110521

Hom.:

8627

Cov.:

AF XY:

0.371

AC XY:

12161

AN XY:

32783

show subpopulations

Gnomad AFR

AF:

0.769

Gnomad AMI

AF:

0.218

Gnomad AMR

AF:

0.382

Gnomad ASJ

AF:

0.235

Gnomad EAS

AF:

0.101

Gnomad SAS

AF:

0.362

Gnomad FIN

AF:

0.124

Gnomad MID

AF:

0.325

Gnomad NFE

AF:

0.242

Gnomad OTH

AF:

0.386

GnomAD3 exomes

AF:

0.291

AC:

47191

AN:

162033

Hom.:

6473

AF XY:

0.280

AC XY:

14489

AN XY:

51753

show subpopulations

Gnomad AFR exome

AF:

0.785

Gnomad AMR exome

AF:

0.372

Gnomad ASJ exome

AF:

0.227

Gnomad EAS exome

AF:

0.104

Gnomad SAS exome

AF:

0.357

Gnomad FIN exome

AF:

0.132

Gnomad NFE exome

AF:

0.237

Gnomad OTH exome

AF:

0.288

GnomAD4 exome

AF:

0.258

AC:

277128

AN:

1075425

Hom.:

28296

Cov.:

AF XY:

0.256

AC XY:

88990

AN XY:

347827

show subpopulations

Gnomad4 AFR exome

AF:

0.791

Gnomad4 AMR exome

AF:

0.370

Gnomad4 ASJ exome

AF:

0.223

Gnomad4 EAS exome

AF:

0.112

Gnomad4 SAS exome

AF:

0.348

Gnomad4 FIN exome

AF:

0.140

Gnomad4 NFE exome

AF:

0.240

Gnomad4 OTH exome

AF:

0.291

GnomAD4 genome

AF:

0.393

AC:

43411

AN:

110574

Hom.:

8631

Cov.:

AF XY:

0.372

AC XY:

12203

AN XY:

32846

show subpopulations

Gnomad4 AFR

AF:

0.769

Gnomad4 AMR

AF:

0.382

Gnomad4 ASJ

AF:

0.235

Gnomad4 EAS

AF:

0.100

Gnomad4 SAS

AF:

0.363

Gnomad4 FIN

AF:

0.124

Gnomad4 NFE

AF:

0.242

Gnomad4 OTH

AF:

0.382

Alfa

AF:

0.323

Hom.:

4740

Bravo

AF:

0.431

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

5.5

DANN

Benign

0.71

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.

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