3-63366863-G-T

Variant names:

• chr3-63366863-G-T
• rs17068377
• NM_001130003.2:c.84+88121G>T

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+88121G>T 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 152,196 control chromosomes in the GnomAD database, including 2,151 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 (2151 hom., cov: 32)
• Consequence: SYNPR NM_001130003.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.254
• 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001130003.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SYNPR	NM_001130003.2	MANE Select	c.84+88121G>T		intron	N/A	NP_001123475.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SYNPR	ENST00000478300.6	TSL:1 MANE Select	c.84+88121G>T		intron	N/A	ENSP00000418994.1
	SYNPR	ENST00000450542.6	TSL:1	c.84+88121G>T		intron	N/A	ENSP00000402121.2
	SYNPR	ENST00000460142.6	TSL:4	n.202+77364G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20510 AN: 152078 Hom.: 2147 Cov.: 32

Gnomad AFR AF: 0.0373

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.570

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.135 AC: 20516 AN: 152196 Hom.: 2151 Cov.: 32 AF XY: 0.139 AC XY: 10329 AN XY: 74402

African (AFR) AF: 0.0372 AC: 1548 AN: 41568

American (AMR) AF: 0.181 AC: 2768 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 635 AN: 3472

East Asian (EAS) AF: 0.571 AC: 2948 AN: 5164

South Asian (SAS) AF: 0.216 AC: 1042 AN: 4822

European-Finnish (FIN) AF: 0.117 AC: 1242 AN: 10594

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

European-Non Finnish (NFE) AF: 0.144 AC: 9815 AN: 67992

Other (OTH) AF: 0.163 AC: 343 AN: 2110

Alfa AF: 0.126 Hom.: 182

Bravo AF: 0.137

Asia WGS AF: 0.372 AC: 1293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.18
DANN	Benign	0.56
PhyloP100		-0.25
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: rs17068377; hg19: chr3-63352539;