14-62083101-G-A

Variant names:

• chr14-62083101-G-A
• rs4902100
• NM_001367656.1:c.1435-1095G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001367656.1(SYT16):​c.1435-1095G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.751 in 152,000 control chromosomes in the GnomAD database, including 43,127 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 0.75 (43127 hom., cov: 31)
• Consequence: SYT16 NM_001367656.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0840
• Publications: 8 publications found

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]

ENSG00000289503 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.875 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001367656.1. 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
	SYT16	NM_001367656.1	MANE Select	c.1435-1095G>A		intron	N/A	NP_001354585.1
	SYT16	NM_001367661.1		c.1435-1095G>A		intron	N/A	NP_001354590.1
	SYT16	NM_001367663.1		c.1435-1095G>A		intron	N/A	NP_001354592.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SYT16	ENST00000683842.1	MANE Select	c.1435-1095G>A		intron	N/A	ENSP00000508274.1
	SYT16	ENST00000568344.5	TSL:1	c.1435-1095G>A		intron	N/A	ENSP00000478637.1
	ENSG00000289503	ENST00000553426.2	TSL:3	n.*372-1095G>A		intron	N/A	ENSP00000508530.1

Frequencies

GnomAD3 genomes AF: 0.751 AC: 114103 AN: 151882 Hom.: 43094 Cov.: 31

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.785

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.897

Gnomad SAS AF: 0.888

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.758

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

GnomAD4 genome AF: 0.751 AC: 114189 AN: 152000 Hom.: 43127 Cov.: 31 AF XY: 0.753 AC XY: 55947 AN XY: 74304

African (AFR) AF: 0.748 AC: 31002 AN: 41444

American (AMR) AF: 0.757 AC: 11578 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.654 AC: 2267 AN: 3468

East Asian (EAS) AF: 0.897 AC: 4634 AN: 5166

South Asian (SAS) AF: 0.889 AC: 4285 AN: 4820

European-Finnish (FIN) AF: 0.701 AC: 7384 AN: 10528

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.743 AC: 50505 AN: 67958

Other (OTH) AF: 0.761 AC: 1609 AN: 2114

Alfa AF: 0.746 Hom.: 143981

Bravo AF: 0.753

Asia WGS AF: 0.885 AC: 3077 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.6
DANN	Benign	0.67
PhyloP100		0.084
Mutation Taster		=100/0	polymorphism (auto)

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: rs4902100; hg19: chr14-62549819;