4-4358935-G-A

Variant names:

• chr4-4358935-G-A
• rs7698300
• ENST00000513555.5:c.-952+10464G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000513555.5(NSG1):​c.-952+10464G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.671 in 151,750 control chromosomes in the GnomAD database, including 34,355 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 0.67 (34355 hom., cov: 30)
• Consequence: NSG1 ENST00000513555.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 6 publications found

Genes affected

NSG1 (HGNC:18790): (neuronal vesicle trafficking associated 1) Predicted to enable clathrin light chain binding activity. Involved in apoptotic process. Located in endoplasmic reticulum. [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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.925 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000513555.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NSG1	ENST00000513555.5	TSL:1	c.-952+10464G>A		intron	N/A	ENSP00000426358.1
	NSG1	ENST00000421177.6	TSL:5	c.-1660+10464G>A		intron	N/A	ENSP00000388823.2

Frequencies

GnomAD3 genomes AF: 0.671 AC: 101741 AN: 151632 Hom.: 34327 Cov.: 30

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.701

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.947

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.726

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.669

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

GnomAD4 genome AF: 0.671 AC: 101823 AN: 151750 Hom.: 34355 Cov.: 30 AF XY: 0.672 AC XY: 49839 AN XY: 74128

African (AFR) AF: 0.666 AC: 27524 AN: 41338

American (AMR) AF: 0.701 AC: 10699 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.672 AC: 2332 AN: 3468

East Asian (EAS) AF: 0.947 AC: 4881 AN: 5152

South Asian (SAS) AF: 0.715 AC: 3420 AN: 4782

European-Finnish (FIN) AF: 0.638 AC: 6694 AN: 10498

Middle Eastern (MID) AF: 0.726 AC: 212 AN: 292

European-Non Finnish (NFE) AF: 0.649 AC: 44081 AN: 67934

Other (OTH) AF: 0.670 AC: 1416 AN: 2112

Alfa AF: 0.659 Hom.: 56079

Bravo AF: 0.678

Asia WGS AF: 0.816 AC: 2836 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.092
DANN	Benign	0.36
PhyloP100		-1.0
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: rs7698300; hg19: chr4-4360662;