chr4-4375440-G-A

Position:

• chr4-4375440-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000513555.5(NSG1):​c.-951-10033G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.834 in 152,184 control chromosomes in the GnomAD database, including 53,552 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 0.83 (53552 hom., cov: 32)
• Consequence: NSG1 ENST00000513555.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130

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]

LOC112268462 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.948 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC112268462	XR_007058004.1	n.244+4825G>A		intron_variant, non_coding_transcript_variant
LOC112268462	XR_002959778.1	n.244+4825G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NSG1	ENST00000513555.5	c.-951-10033G>A		intron_variant		1		P1
NSG1	ENST00000421177.6	c.-1659-5543G>A		intron_variant		5		P1

Frequencies

GnomAD3 genomes AF: 0.834 AC: 126874 AN: 152066 Hom.: 53493 Cov.: 32

Gnomad AFR AF: 0.956

Gnomad AMI AF: 0.740

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.828

Gnomad EAS AF: 0.944

Gnomad SAS AF: 0.835

Gnomad FIN AF: 0.793

Gnomad MID AF: 0.739

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.797

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

GnomAD4 genome AF: 0.834 AC: 126985 AN: 152184 Hom.: 53552 Cov.: 32 AF XY: 0.832 AC XY: 61898 AN XY: 74388

Gnomad4 AFR AF: 0.956

Gnomad4 AMR AF: 0.747

Gnomad4 ASJ AF: 0.828

Gnomad4 EAS AF: 0.943

Gnomad4 SAS AF: 0.835

Gnomad4 FIN AF: 0.793

Gnomad4 NFE AF: 0.781

Gnomad4 OTH AF: 0.800

Alfa AF: 0.807 Hom.: 11117

Bravo AF: 0.836

Asia WGS AF: 0.888 AC: 3089 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.6
DANN	Benign	0.52

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: rs4318596; hg19: chr4-4377167;