chr3-63368874-C-G

Variant names:

• chr3-63368874-C-G
• rs12638620
• NM_001130003.2:c.84+90132C>G

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+90132C>G 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 152,168 control chromosomes in the GnomAD database, including 2,108 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 (2108 hom., cov: 32)
• Consequence: SYNPR NM_001130003.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.453
• Publications: 1 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=-0.9).
• 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 rank	MANE	Protein	UniProt
SYNPR	NM_001130003.2	c.84+90132C>G		intron_variant	Intron 2 of 5	ENST00000478300.6	NP_001123475.1
SYNPR	XM_017005731.1	c.133-111958C>G		intron_variant	Intron 2 of 5		XP_016861220.1
SYNPR	XM_017005732.3	c.84+90132C>G		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+90132C>G		intron_variant	Intron 2 of 5	1	NM_001130003.2	ENSP00000418994.1

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20424 AN: 152050 Hom.: 2104 Cov.: 32

Gnomad AFR AF: 0.0372

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.134 AC: 20430 AN: 152168 Hom.: 2108 Cov.: 32 AF XY: 0.138 AC XY: 10279 AN XY: 74370

African (AFR) AF: 0.0371 AC: 1542 AN: 41560

American (AMR) AF: 0.181 AC: 2767 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 635 AN: 3470

East Asian (EAS) AF: 0.557 AC: 2871 AN: 5150

South Asian (SAS) AF: 0.215 AC: 1037 AN: 4816

European-Finnish (FIN) AF: 0.117 AC: 1241 AN: 10582

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

European-Non Finnish (NFE) AF: 0.144 AC: 9817 AN: 68002

Other (OTH) AF: 0.164 AC: 345 AN: 2110

Alfa AF: 0.121 Hom.: 170

Bravo AF: 0.137

Asia WGS AF: 0.370 AC: 1283 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.67
PhyloP100		-0.45
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: rs12638620; hg19: chr3-63354550;