3-63468934-T-C

Variant names:

• chr3-63468934-T-C
• rs11708068
• NM_001130003.2:c.85-11898T>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.85-11898T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 152,108 control chromosomes in the GnomAD database, including 6,552 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 0.29 (6552 hom., cov: 32)
• Consequence: SYNPR NM_001130003.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.113
• Publications: 2 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]

SYNPR-AS1 (HGNC:40774): (SYNPR antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SYNPR	NM_001130003.2	c.85-11898T>C		intron_variant	Intron 2 of 5	ENST00000478300.6	NP_001123475.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SYNPR	ENST00000478300.6	c.85-11898T>C		intron_variant	Intron 2 of 5	1	NM_001130003.2	ENSP00000418994.1

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43643 AN: 151990 Hom.: 6544 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.287 AC: 43680 AN: 152108 Hom.: 6552 Cov.: 32 AF XY: 0.289 AC XY: 21482 AN XY: 74348

African (AFR) AF: 0.333 AC: 13804 AN: 41510

American (AMR) AF: 0.263 AC: 4013 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 849 AN: 3472

East Asian (EAS) AF: 0.431 AC: 2213 AN: 5136

South Asian (SAS) AF: 0.302 AC: 1456 AN: 4822

European-Finnish (FIN) AF: 0.293 AC: 3096 AN: 10580

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17279 AN: 67988

Other (OTH) AF: 0.268 AC: 567 AN: 2112

Alfa AF: 0.280 Hom.: 1146

Bravo AF: 0.287

Asia WGS AF: 0.341 AC: 1186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.63
PhyloP100		-0.11
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: rs11708068; hg19: chr3-63454610;