14-61930727-T-C

Variant names:

• chr14-61930727-T-C
• rs6573406
• NM_001367656.1:c.-324-39405T>C

Variant summary

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

The NM_001367656.1(SYT16):​c.-324-39405T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 151,722 control chromosomes in the GnomAD database, including 2,054 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 (2054 hom., cov: 32)
• Consequence: SYT16 NM_001367656.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.337
• Publications: 1 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SYT16	NM_001367656.1	c.-324-39405T>C		intron_variant	Intron 1 of 7	ENST00000683842.1	NP_001354585.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SYT16	ENST00000683842.1	c.-324-39405T>C		intron_variant	Intron 1 of 7		NM_001367656.1	ENSP00000508274.1
SYT16	ENST00000636133.1	c.14-39405T>C		intron_variant	Intron 1 of 3	5		ENSP00000490266.1
SYT16	ENST00000554138.1	n.393-39405T>C		intron_variant	Intron 1 of 1	3
SYT16	ENST00000554436.1	n.482+33372T>C		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20624 AN: 151604 Hom.: 2052 Cov.: 32

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.0867

Gnomad EAS AF: 0.0434

Gnomad SAS AF: 0.0538

Gnomad FIN AF: 0.0920

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.0690

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.136 AC: 20652 AN: 151722 Hom.: 2054 Cov.: 32 AF XY: 0.136 AC XY: 10073 AN XY: 74114

African (AFR) AF: 0.269 AC: 11105 AN: 41270

American (AMR) AF: 0.178 AC: 2708 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.0867 AC: 301 AN: 3470

East Asian (EAS) AF: 0.0433 AC: 222 AN: 5128

South Asian (SAS) AF: 0.0537 AC: 258 AN: 4806

European-Finnish (FIN) AF: 0.0920 AC: 968 AN: 10524

Middle Eastern (MID) AF: 0.137 AC: 40 AN: 292

European-Non Finnish (NFE) AF: 0.0690 AC: 4692 AN: 67972

Other (OTH) AF: 0.123 AC: 260 AN: 2106

Alfa AF: 0.0940 Hom.: 1982

Bravo AF: 0.151

Asia WGS AF: 0.0670 AC: 233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.32
PhyloP100		0.34
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs6573406; hg19: chr14-62397445;