X-38000257-T-G

Position:

• chrX-38000257-T-G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000465127.1(ENSG00000250349):​c.171+574257T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.65 (16573 hom., 21622 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000250349 ENST00000465127.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.544

Genes affected

ENSG00000250349 (HGNC:):

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]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SYTL5	XM_011544001.3	c.-356-33277T>G		intron_variant			XP_011542303.1
SYTL5	XM_011544002.3	c.-356-33277T>G		intron_variant			XP_011542304.1
SYTL5	XM_017029972.1	c.-356-33277T>G		intron_variant			XP_016885461.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000250349	ENST00000465127.1	c.171+574257T>G		intron_variant		5		ENSP00000417050.1

Frequencies

GnomAD3 genomes AF: 0.650 AC: 72155 AN: 110975 Hom.: 16574 Cov.: 23 AF XY: 0.649 AC XY: 21576 AN XY: 33225

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.688

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.723

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.635

Gnomad MID AF: 0.587

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.651

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.650 AC: 72196 AN: 111025 Hom.: 16573 Cov.: 23 AF XY: 0.650 AC XY: 21622 AN XY: 33285

Gnomad4 AFR AF: 0.702

Gnomad4 AMR AF: 0.689

Gnomad4 ASJ AF: 0.510

Gnomad4 EAS AF: 0.723

Gnomad4 SAS AF: 0.688

Gnomad4 FIN AF: 0.635

Gnomad4 NFE AF: 0.615

Gnomad4 OTH AF: 0.645

Alfa AF: 0.626 Hom.: 68001

Bravo AF: 0.659

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.8
DANN	Benign	0.62

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

Other links and lift over

dbSNP: rs761913; hg19: chrX-37859510;