14-62051630-C-G

Variant names:

• chr14-62051630-C-G
• rs6573416
• NM_001367656.1:c.524-17973C>G

Variant summary

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

The NM_001367656.1(SYT16):​c.524-17973C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,188 control chromosomes in the GnomAD database, including 2,353 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 0.17 (2353 hom., cov: 33)
• Consequence: SYT16 NM_001367656.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.306
• Publications: 2 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SYT16	NM_001367656.1	c.524-17973C>G		intron_variant	Intron 3 of 7	ENST00000683842.1	NP_001354585.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SYT16	ENST00000683842.1	c.524-17973C>G		intron_variant	Intron 3 of 7		NM_001367656.1	ENSP00000508274.1
SYT16	ENST00000568344.5	c.524-17973C>G		intron_variant	Intron 1 of 5	1		ENSP00000478637.1
SYT16	ENST00000636133.1	c.194-17973C>G		intron_variant	Intron 2 of 3	5		ENSP00000490266.1
SYT16	ENST00000555409.1	n.524-17973C>G		intron_variant	Intron 1 of 6	5		ENSP00000451035.1

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25285 AN: 152070 Hom.: 2354 Cov.: 33

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.0522

Gnomad EAS AF: 0.0708

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.166 AC: 25303 AN: 152188 Hom.: 2353 Cov.: 33 AF XY: 0.165 AC XY: 12280 AN XY: 74402

African (AFR) AF: 0.258 AC: 10710 AN: 41506

American (AMR) AF: 0.116 AC: 1779 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0522 AC: 181 AN: 3470

East Asian (EAS) AF: 0.0705 AC: 366 AN: 5188

South Asian (SAS) AF: 0.285 AC: 1373 AN: 4820

European-Finnish (FIN) AF: 0.104 AC: 1104 AN: 10596

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9351 AN: 67998

Other (OTH) AF: 0.134 AC: 283 AN: 2116

Alfa AF: 0.0563 Hom.: 55

Bravo AF: 0.168

Asia WGS AF: 0.179 AC: 623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.3
DANN	Benign	0.62
PhyloP100		-0.31
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: rs6573416; hg19: chr14-62518348;