14-61996148-C-T

Variant names:

• chr14-61996148-C-T
• rs781569552
• NM_001367656.1:c.129C>T

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2 BP4_Moderate BP7

The NM_001367656.1(SYT16):​c.129C>T​(p.Ser43Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: SYT16 NM_001367656.1 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.799
• Publications: 0 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: Likely_benign. The variant received -1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BP7: Synonymous conserved (PhyloP=0.799 with no splicing effect.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SYT16	NM_001367656.1	MANE Select	c.129C>T	p.Ser43Ser	synonymous	Exon 3 of 8	NP_001354585.1	Q17RD7-1
	SYT16	NM_001367661.1		c.129C>T	p.Ser43Ser	synonymous	Exon 4 of 9	NP_001354590.1	Q17RD7-1
	SYT16	NM_001367663.1		c.129C>T	p.Ser43Ser	synonymous	Exon 3 of 8	NP_001354592.1	Q17RD7-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SYT16	ENST00000683842.1	MANE Select	c.129C>T	p.Ser43Ser	synonymous	Exon 3 of 8	ENSP00000508274.1	Q17RD7-1
	SYT16	ENST00000568344.5	TSL:1	c.129C>T	p.Ser43Ser	synonymous	Exon 1 of 6	ENSP00000478637.1	Q17RD7-1
	SYT16	ENST00000883052.1		c.129C>T	p.Ser43Ser	synonymous	Exon 3 of 8	ENSP00000553111.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 58

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	9.3
DANN	Benign	0.61
PhyloP100		0.80
PromoterAI		0.0083	Neutral

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: rs781569552; hg19: chr14-62462866;