5-174193283-T-C

Variant names:

• chr5-174193283-T-C
• rs7705993
• ENST00000521585.5:c.214-11917T>C

Variant summary

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

The ENST00000521585.5(NSG2):​c.214-11917T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 151,958 control chromosomes in the GnomAD database, including 16,843 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 0.47 (16843 hom., cov: 32)
• Consequence: NSG2 ENST00000521585.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.145
• Publications: 3 publications found

Genes affected

NSG2 (HGNC:24955): (neuronal vesicle trafficking associated 2) Predicted to enable clathrin light chain binding activity. Predicted to be involved in clathrin coat assembly and endosomal transport. Located in Golgi apparatus. [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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000521585.5. 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
	NSG2	ENST00000521585.5	TSL:4	c.214-11917T>C		intron	N/A	ENSP00000429863.1

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71078 AN: 151840 Hom.: 16834 Cov.: 32

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.468 AC: 71118 AN: 151958 Hom.: 16843 Cov.: 32 AF XY: 0.459 AC XY: 34076 AN XY: 74254

African (AFR) AF: 0.504 AC: 20861 AN: 41422

American (AMR) AF: 0.424 AC: 6479 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.504 AC: 1750 AN: 3472

East Asian (EAS) AF: 0.314 AC: 1615 AN: 5140

South Asian (SAS) AF: 0.381 AC: 1834 AN: 4818

European-Finnish (FIN) AF: 0.384 AC: 4039 AN: 10526

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.485 AC: 32942 AN: 67984

Other (OTH) AF: 0.483 AC: 1018 AN: 2108

Alfa AF: 0.478 Hom.: 58249

Bravo AF: 0.471

Asia WGS AF: 0.369 AC: 1288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.87
DANN	Benign	0.39
PhyloP100		-0.14
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7705993; hg19: chr5-173620286;