rs10510896

Positions:

• chr3-63369416-G-A

Variant summary

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

The NM_001130003.2(SYNPR):​c.84+90674G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,222 control chromosomes in the GnomAD database, including 2,094 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 (2094 hom., cov: 32)
• Consequence: SYNPR NM_001130003.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.451

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SYNPR	NM_001130003.2	c.84+90674G>A		intron_variant		ENST00000478300.6	NP_001123475.1
SYNPR	XM_017005731.1	c.133-111416G>A		intron_variant			XP_016861220.1
SYNPR	XM_017005732.3	c.84+90674G>A		intron_variant			XP_016861221.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SYNPR	ENST00000478300.6	c.84+90674G>A		intron_variant		1	NM_001130003.2	ENSP00000418994	P1

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20369 AN: 152104 Hom.: 2090 Cov.: 32

Gnomad AFR AF: 0.0371

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.213

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: 0.134 AC: 20375 AN: 152222 Hom.: 2094 Cov.: 32 AF XY: 0.138 AC XY: 10254 AN XY: 74420

Gnomad4 AFR AF: 0.0370

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.557

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.163

Alfa AF: 0.142 Hom.: 867

Bravo AF: 0.136

Asia WGS AF: 0.370 AC: 1286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.27
DANN	Benign	0.76

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: rs10510896; hg19: chr3-63355092;