X-38000257-T-G

Variant names:

• chrX-38000257-T-G
• rs761913
• ENST00000465127.1:c.171+574257T>G

Variant summary

Our verdict is Likely benign. The variant received -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
• Publications: 0 publications found

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

Our verdict: Likely_benign. The variant received -4 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000465127.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000250349	ENST00000465127.1	TSL:5	c.171+574257T>G		intron	N/A	ENSP00000417050.1

Frequencies

GnomAD3 genomes AF: 0.650 AC: 72155 AN: 110975 Hom.: 16574 Cov.: 23

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

African (AFR) AF: 0.702 AC: 21446 AN: 30532

American (AMR) AF: 0.689 AC: 7261 AN: 10542

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1348 AN: 2643

East Asian (EAS) AF: 0.723 AC: 2531 AN: 3502

South Asian (SAS) AF: 0.688 AC: 1807 AN: 2627

European-Finnish (FIN) AF: 0.635 AC: 3750 AN: 5902

Middle Eastern (MID) AF: 0.596 AC: 127 AN: 213

European-Non Finnish (NFE) AF: 0.615 AC: 32507 AN: 52883

Other (OTH) AF: 0.645 AC: 973 AN: 1508

Alfa AF: 0.633 Hom.: 91578

Bravo AF: 0.659

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.8
DANN	Benign	0.62
PhyloP100		-0.54

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

Other links and lift over

dbSNP: rs761913; hg19: chrX-37859510;