3-63453210-T-C

Variant names:

• chr3-63453210-T-C
• rs1975649
• NM_001130003.2:c.85-27622T>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.85-27622T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.737 in 152,096 control chromosomes in the GnomAD database, including 42,377 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 0.74 (42377 hom., cov: 32)
• Consequence: SYNPR NM_001130003.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990
• Publications: 4 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SYNPR	NM_001130003.2	c.85-27622T>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.85-27622T>C		intron_variant	Intron 2 of 5	1	NM_001130003.2	ENSP00000418994.1

Frequencies

GnomAD3 genomes AF: 0.737 AC: 112026 AN: 151978 Hom.: 42329 Cov.: 32

Gnomad AFR AF: 0.913

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.633

Gnomad EAS AF: 0.659

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.717

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

GnomAD4 genome AF: 0.737 AC: 112133 AN: 152096 Hom.: 42377 Cov.: 32 AF XY: 0.733 AC XY: 54454 AN XY: 74316

African (AFR) AF: 0.913 AC: 37905 AN: 41530

American (AMR) AF: 0.668 AC: 10205 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.633 AC: 2195 AN: 3470

East Asian (EAS) AF: 0.658 AC: 3386 AN: 5142

South Asian (SAS) AF: 0.672 AC: 3243 AN: 4824

European-Finnish (FIN) AF: 0.673 AC: 7118 AN: 10576

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.674 AC: 45777 AN: 67962

Other (OTH) AF: 0.713 AC: 1509 AN: 2116

Alfa AF: 0.686 Hom.: 66105

Bravo AF: 0.745

Asia WGS AF: 0.702 AC: 2443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.52
PhyloP100		-0.099
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: rs1975649; hg19: chr3-63438886;