3-63273833-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_017005731.1(SYNPR):c.132+21247A>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 XM_017005731.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.433

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
SYNPR	XM_017005731.1	c.132+21247A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SYNPR	ENST00000478456.5	n.287+6384A>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.660

Gnomad4 AMR AF: 0.785

Gnomad4 ASJ AF: 0.859

Gnomad4 EAS AF: 0.494

Gnomad4 SAS AF: 0.769

Gnomad4 FIN AF: 0.821

Gnomad4 NFE AF: 0.826

Gnomad4 OTH AF: 0.771

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9311863; hg19: chr3-63259509;