rs529989

Variant names:

• chr1-114135326-C-A
• rs529989
• NM_001253772.2:c.1071+2169G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-114135326-C-A
• chr1-114135326-C-G
• chr1-114135326-C-T

Variant summary

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

The NM_001253772.2(SYT6):​c.1071+2169G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.592 in 151,900 control chromosomes in the GnomAD database, including 26,841 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 0.59 (26841 hom., cov: 31)
• Consequence: SYT6 NM_001253772.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 4 publications found

Genes affected

SYT6 (HGNC:18638): (synaptotagmin 6) The protein encoded by this gene belongs to the synaptotagmin family. Synaptotagmins share a common domain structure that includes a transmembrane domain and a cytoplasmic region composed of 2 C2 domains, and are involved in calcium-dependent exocytosis of synaptic vesicles. This protein has been shown to be a key component of the secretory machinery involved in acrosomal exocytosis. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Dec 2011]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SYT6	NM_001253772.2	c.1071+2169G>T		intron_variant	Intron 3 of 7	ENST00000610222.3	NP_001240701.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SYT6	ENST00000610222.3	c.1071+2169G>T		intron_variant	Intron 3 of 7	5	NM_001253772.2	ENSP00000476396.1

Frequencies

GnomAD3 genomes AF: 0.592 AC: 89834 AN: 151782 Hom.: 26828 Cov.: 31

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.768

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.592 AC: 89894 AN: 151900 Hom.: 26841 Cov.: 31 AF XY: 0.598 AC XY: 44422 AN XY: 74234

African (AFR) AF: 0.595 AC: 24638 AN: 41416

American (AMR) AF: 0.662 AC: 10105 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.496 AC: 1722 AN: 3472

East Asian (EAS) AF: 0.767 AC: 3942 AN: 5140

South Asian (SAS) AF: 0.654 AC: 3142 AN: 4806

European-Finnish (FIN) AF: 0.638 AC: 6728 AN: 10538

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.555 AC: 37735 AN: 67936

Other (OTH) AF: 0.592 AC: 1252 AN: 2116

Alfa AF: 0.569 Hom.: 45886

Bravo AF: 0.590

Asia WGS AF: 0.713 AC: 2476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.067
DANN	Benign	0.38
PhyloP100		-1.0
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: rs529989; hg19: chr1-114677948;