rs2784505

Positions:

• chr14-61965295-A-G

Variant summary

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

The NM_001367656.1(SYT16):​c.-324-4837A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,154 control chromosomes in the GnomAD database, including 2,908 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 0.14 (2908 hom., cov: 32)
• Consequence: SYT16 NM_001367656.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

Genes affected

SYT16 (HGNC:23142): (synaptotagmin 16) Predicted to enable identical protein binding activity and phospholipid binding activity. Predicted to be involved in exocytosis. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SYT16	NM_001367656.1	c.-324-4837A>G		intron_variant		ENST00000683842.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SYT16	ENST00000683842.1	c.-324-4837A>G		intron_variant			NM_001367656.1	P1
SYT16	ENST00000636133.1	c.14-4837A>G		intron_variant		5
SYT16	ENST00000554138.1	n.393-4837A>G		intron_variant, non_coding_transcript_variant		3
SYT16	ENST00000554436.1	n.483-4837A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21762 AN: 152036 Hom.: 2897 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.0867

Gnomad ASJ AF: 0.0918

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.0611

Gnomad FIN AF: 0.0486

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0674

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.143 AC: 21805 AN: 152154 Hom.: 2908 Cov.: 32 AF XY: 0.140 AC XY: 10405 AN XY: 74398

Gnomad4 AFR AF: 0.348

Gnomad4 AMR AF: 0.0866

Gnomad4 ASJ AF: 0.0918

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.0603

Gnomad4 FIN AF: 0.0486

Gnomad4 NFE AF: 0.0674

Gnomad4 OTH AF: 0.118

Alfa AF: 0.0794 Hom.: 733

Bravo AF: 0.152

Asia WGS AF: 0.0600 AC: 211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.15
DANN	Benign	0.37

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2784505; hg19: chr14-62432013;