3-63364793-A-G

Variant names:

• chr3-63364793-A-G
• rs13068980
• NM_001130003.2:c.84+86051A>G

Variant summary

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

The NM_001130003.2(SYNPR):​c.84+86051A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,088 control chromosomes in the GnomAD database, including 2,149 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 0.13 (2149 hom., cov: 32)
• Consequence: SYNPR NM_001130003.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.856
• Publications: 0 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SYNPR	NM_001130003.2	c.84+86051A>G		intron_variant	Intron 2 of 5	ENST00000478300.6	NP_001123475.1
SYNPR	XM_017005731.1	c.132+112207A>G		intron_variant	Intron 2 of 5		XP_016861220.1
SYNPR	XM_017005732.3	c.84+86051A>G		intron_variant	Intron 2 of 5		XP_016861221.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SYNPR	ENST00000478300.6	c.84+86051A>G		intron_variant	Intron 2 of 5	1	NM_001130003.2	ENSP00000418994.1

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20518 AN: 151970 Hom.: 2145 Cov.: 32

Gnomad AFR AF: 0.0374

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.570

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.135 AC: 20524 AN: 152088 Hom.: 2149 Cov.: 32 AF XY: 0.139 AC XY: 10337 AN XY: 74356

African (AFR) AF: 0.0373 AC: 1550 AN: 41532

American (AMR) AF: 0.182 AC: 2771 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 635 AN: 3470

East Asian (EAS) AF: 0.571 AC: 2936 AN: 5142

South Asian (SAS) AF: 0.217 AC: 1046 AN: 4816

European-Finnish (FIN) AF: 0.117 AC: 1240 AN: 10584

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.145 AC: 9830 AN: 67968

Other (OTH) AF: 0.162 AC: 341 AN: 2106

Alfa AF: 0.147 Hom.: 5927

Bravo AF: 0.137

Asia WGS AF: 0.373 AC: 1296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.4
DANN	Benign	0.70
PhyloP100		0.86
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: rs13068980; hg19: chr3-63350469;