6-158725839-C-T

Position:

• chr6-158725839-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001242394.2(SYTL3):​c.855+202C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.601 in 749,850 control chromosomes in the GnomAD database, including 142,219 homozygotes. 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 0.66 (34979 hom., cov: 32)
  • Exomes 𝑓: 0.59 (107240 hom.)
• Consequence: SYTL3 NM_001242394.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950

Genes affected

SYTL3 (HGNC:15587): (synaptotagmin like 3) The protein encoded by this gene belongs to a family of peripheral membrane proteins that play a role in vesicular trafficking. This protein binds phospholipids in the presence of calcium ions. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2016]

AMZ2P2 (HGNC:38072): (AMZ2 pseudogene 2)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.872 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SYTL3	NM_001242394.2	c.855+202C>T		intron_variant		ENST00000611299.5	NP_001229323.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SYTL3	ENST00000611299.5	c.855+202C>T		intron_variant		5	NM_001242394.2	ENSP00000483936	P1
AMZ2P2	ENST00000406819.2	n.965G>A		non_coding_transcript_exon_variant	1/1
SYTL3	ENST00000360448.8	c.855+202C>T		intron_variant		5		ENSP00000353631	P1
SYTL3	ENST00000367081.7	c.651+202C>T		intron_variant		5		ENSP00000356048

Frequencies

GnomAD3 genomes AF: 0.659 AC: 100119 AN: 152006 Hom.: 34925 Cov.: 32

Gnomad AFR AF: 0.879

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.634

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.637

GnomAD4 exome AF: 0.586 AC: 350258 AN: 597726 Hom.: 107240 Cov.: 7 AF XY: 0.591 AC XY: 189074 AN XY: 320028

Gnomad4 AFR exome AF: 0.887

Gnomad4 AMR exome AF: 0.429

Gnomad4 ASJ exome AF: 0.594

Gnomad4 EAS exome AF: 0.159

Gnomad4 SAS exome AF: 0.674

Gnomad4 FIN exome AF: 0.637

Gnomad4 NFE exome AF: 0.605

Gnomad4 OTH exome AF: 0.598

GnomAD4 genome AF: 0.659 AC: 100223 AN: 152124 Hom.: 34979 Cov.: 32 AF XY: 0.654 AC XY: 48632 AN XY: 74354

Gnomad4 AFR AF: 0.880

Gnomad4 AMR AF: 0.499

Gnomad4 ASJ AF: 0.601

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.666

Gnomad4 FIN AF: 0.634

Gnomad4 NFE AF: 0.603

Gnomad4 OTH AF: 0.633

Alfa AF: 0.603 Hom.: 47857

Bravo AF: 0.651

Asia WGS AF: 0.474 AC: 1649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.5
DANN	Benign	0.60

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: rs6455600; hg19: chr6-159146871;