3-63453210-T-C

Position:

• chr3-63453210-T-C

Variant summary

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

The NM_001130003.2(SYNPR):​c.85-27622T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.737 in 152,096 control chromosomes in the GnomAD database, including 42,377 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 0.74 (42377 hom., cov: 32)
• Consequence: SYNPR NM_001130003.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990

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]

SYNPR (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SYNPR	NM_001130003.2	c.85-27622T>C		intron_variant		ENST00000478300.6	NP_001123475.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SYNPR	ENST00000478300.6	c.85-27622T>C		intron_variant		1	NM_001130003.2	ENSP00000418994.1

Frequencies

GnomAD3 genomes AF: 0.737 AC: 112026 AN: 151978 Hom.: 42329 Cov.: 32

Gnomad AFR AF: 0.913

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.633

Gnomad EAS AF: 0.659

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.717

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

GnomAD4 genome AF: 0.737 AC: 112133 AN: 152096 Hom.: 42377 Cov.: 32 AF XY: 0.733 AC XY: 54454 AN XY: 74316

Gnomad4 AFR AF: 0.913

Gnomad4 AMR AF: 0.668

Gnomad4 ASJ AF: 0.633

Gnomad4 EAS AF: 0.658

Gnomad4 SAS AF: 0.672

Gnomad4 FIN AF: 0.673

Gnomad4 NFE AF: 0.674

Gnomad4 OTH AF: 0.713

Alfa AF: 0.677 Hom.: 46129

Bravo AF: 0.745

Asia WGS AF: 0.702 AC: 2443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.52

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

Publications

LitVar

Other links and lift over

dbSNP: rs1975649; hg19: chr3-63438886;