5-174198151-T-C

Variant names:

• chr5-174198151-T-C
• rs6863418
• ENST00000521585.5:c.214-7049T>C

Variant summary

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

The ENST00000521585.5(NSG2):​c.214-7049T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.61 in 152,162 control chromosomes in the GnomAD database, including 29,224 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 0.61 (29224 hom., cov: 34)
• Consequence: NSG2 ENST00000521585.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.877 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NSG2	ENST00000521585.5	TSL:4	c.214-7049T>C		intron	N/A	ENSP00000429863.1

Frequencies

GnomAD3 genomes AF: 0.611 AC: 92845 AN: 152044 Hom.: 29215 Cov.: 34

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.855

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.898

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.650

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.610 AC: 92891 AN: 152162 Hom.: 29224 Cov.: 34 AF XY: 0.608 AC XY: 45256 AN XY: 74382

African (AFR) AF: 0.470 AC: 19513 AN: 41500

American (AMR) AF: 0.704 AC: 10771 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.651 AC: 2257 AN: 3468

East Asian (EAS) AF: 0.898 AC: 4658 AN: 5186

South Asian (SAS) AF: 0.755 AC: 3635 AN: 4814

European-Finnish (FIN) AF: 0.524 AC: 5545 AN: 10586

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.650 AC: 44161 AN: 67988

Other (OTH) AF: 0.647 AC: 1367 AN: 2112

Alfa AF: 0.642 Hom.: 43928

Bravo AF: 0.619

Asia WGS AF: 0.830 AC: 2885 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.72
PhyloP100		-1.0
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: rs6863418; hg19: chr5-173625154;