NM_001130003.2:c.84+91566T>C

Variant names:

• chr3-63370308-T-C
• rs17068392
• NM_001130003.2:c.84+91566T>C

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+91566T>C 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 152,212 control chromosomes in the GnomAD database, including 2,120 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 (2120 hom., cov: 32)
• Consequence: SYNPR NM_001130003.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.349
• 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=-0.54).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SYNPR	NM_001130003.2	c.84+91566T>C		intron_variant	Intron 2 of 5	ENST00000478300.6	NP_001123475.1
SYNPR	XM_017005731.1	c.133-110524T>C		intron_variant	Intron 2 of 5		XP_016861220.1
SYNPR	XM_017005732.3	c.84+91566T>C		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+91566T>C		intron_variant	Intron 2 of 5	1	NM_001130003.2	ENSP00000418994.1

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20486 AN: 152096 Hom.: 2116 Cov.: 32

Gnomad AFR AF: 0.0374

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.145

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: 20493 AN: 152212 Hom.: 2120 Cov.: 32 AF XY: 0.139 AC XY: 10311 AN XY: 74408

African (AFR) AF: 0.0373 AC: 1549 AN: 41564

American (AMR) AF: 0.181 AC: 2772 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 647 AN: 3470

East Asian (EAS) AF: 0.559 AC: 2877 AN: 5146

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

European-Finnish (FIN) AF: 0.117 AC: 1242 AN: 10592

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

European-Non Finnish (NFE) AF: 0.145 AC: 9842 AN: 68018

Other (OTH) AF: 0.163 AC: 344 AN: 2112

Alfa AF: 0.126 Hom.: 178

Bravo AF: 0.137

Asia WGS AF: 0.372 AC: 1293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	15
DANN	Benign	0.85
PhyloP100		0.35
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: rs17068392; hg19: chr3-63355984;