rs7698300

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr4-4358935-G-A
• chr4-4358935-G-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NSG1	ENST00000513555.5	c.-952+10464G>A		intron_variant	Intron 1 of 7	1		ENSP00000426358.1
NSG1	ENST00000421177.6	c.-1660+10464G>A		intron_variant	Intron 1 of 8	5		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

Gnomad4 AFR AF: 0.666

Gnomad4 AMR AF: 0.701

Gnomad4 ASJ AF: 0.672

Gnomad4 EAS AF: 0.947

Gnomad4 SAS AF: 0.715

Gnomad4 FIN AF: 0.638

Gnomad4 NFE AF: 0.649

Gnomad4 OTH AF: 0.670

Alfa AF: 0.658 Hom.: 44077

Bravo AF: 0.678

Asia WGS AF: 0.816 AC: 2836 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.092
DANN	Benign	0.36

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

Publications

LitVar

Other links and lift over

dbSNP: rs7698300; hg19: chr4-4360662;