16-19233102-A-G

Variant names:

• chr16-19233102-A-G
• rs6497337
• NM_016524.4:c.1228+8264A>G

Variant summary

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

The NM_016524.4(SYT17):​c.1228+8264A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.747 in 152,010 control chromosomes in the GnomAD database, including 43,505 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 (43505 hom., cov: 31)
• Consequence: SYT17 NM_016524.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0630
• Publications: 3 publications found

Genes affected

SYT17 (HGNC:24119): (synaptotagmin 17) Predicted to enable several functions, including calcium ion binding activity; phospholipid binding activity; and syntaxin binding activity. Involved in positive regulation of dendrite extension. Predicted to be located in trans-Golgi network. Predicted to be active in exocytic vesicle and plasma 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016524.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SYT17	NM_016524.4	MANE Select	c.1228+8264A>G		intron	N/A	NP_057608.2
	SYT17	NM_001308157.2		c.1216+8264A>G		intron	N/A	NP_001295086.1	H3BN78
	SYT17	NM_001330509.2		c.1045+8264A>G		intron	N/A	NP_001317438.1	H3BRH9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SYT17	ENST00000355377.7	TSL:1 MANE Select	c.1228+8264A>G		intron	N/A	ENSP00000347538.2	Q9BSW7
	SYT17	ENST00000562034.5	TSL:1	c.1045+8264A>G		intron	N/A	ENSP00000456252.1	H3BRH9
	SYT17	ENST00000971661.1		c.1222+8264A>G		intron	N/A	ENSP00000641720.1

Frequencies

GnomAD3 genomes AF: 0.747 AC: 113436 AN: 151892 Hom.: 43432 Cov.: 31

Gnomad AFR AF: 0.884

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.991

Gnomad SAS AF: 0.853

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.747 AC: 113569 AN: 152010 Hom.: 43505 Cov.: 31 AF XY: 0.751 AC XY: 55801 AN XY: 74282

African (AFR) AF: 0.884 AC: 36709 AN: 41528

American (AMR) AF: 0.768 AC: 11729 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2438 AN: 3472

East Asian (EAS) AF: 0.991 AC: 5113 AN: 5162

South Asian (SAS) AF: 0.852 AC: 4105 AN: 4818

European-Finnish (FIN) AF: 0.623 AC: 6556 AN: 10522

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.659 AC: 44776 AN: 67916

Other (OTH) AF: 0.718 AC: 1517 AN: 2112

Alfa AF: 0.699 Hom.: 77706

Bravo AF: 0.762

Asia WGS AF: 0.922 AC: 3207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.1
DANN	Benign	0.38
PhyloP100		-0.063
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: rs6497337; hg19: chr16-19244424;