3-63273833-A-T

Variant names:

• chr3-63273833-A-T
• rs9311863
• ENST00000478456.5:n.287+6384A>T

Variant summary

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

The ENST00000478456.5(SYNPR):​n.287+6384A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.763 in 152,090 control chromosomes in the GnomAD database, including 44,999 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 0.76 (44999 hom., cov: 32)
• Consequence: SYNPR ENST00000478456.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.433
• Publications: 4 publications found

Genes affected

SYNPR (HGNC:16507): (synaptoporin) Predicted to be located in neuron projection and synaptic vesicle. Predicted to be integral component of membrane. Predicted to be active in synaptic vesicle membrane. Predicted to be integral component of synaptic vesicle 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.82 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SYNPR	XM_017005731.1	c.132+21247A>T		intron_variant	Intron 2 of 5		XP_016861220.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SYNPR	ENST00000478456.5	n.287+6384A>T		intron_variant	Intron 3 of 4	4

Frequencies

GnomAD3 genomes AF: 0.764 AC: 116039 AN: 151972 Hom.: 44980 Cov.: 32

Gnomad AFR AF: 0.660

Gnomad AMI AF: 0.878

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.859

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.769

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.826

Gnomad OTH AF: 0.777

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

GnomAD4 genome AF: 0.763 AC: 116114 AN: 152090 Hom.: 44999 Cov.: 32 AF XY: 0.762 AC XY: 56653 AN XY: 74336

African (AFR) AF: 0.660 AC: 27371 AN: 41468

American (AMR) AF: 0.785 AC: 11988 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.859 AC: 2980 AN: 3468

East Asian (EAS) AF: 0.494 AC: 2547 AN: 5158

South Asian (SAS) AF: 0.769 AC: 3712 AN: 4828

European-Finnish (FIN) AF: 0.821 AC: 8686 AN: 10580

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.826 AC: 56144 AN: 67992

Other (OTH) AF: 0.771 AC: 1630 AN: 2114

Alfa AF: 0.802 Hom.: 6101

Bravo AF: 0.755

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.6
DANN	Benign	0.78
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs9311863; hg19: chr3-63259509;