5-174198151-T-C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

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
NSG2	ENST00000521585.5	c.214-7049T>C		intron_variant	Intron 3 of 4	4		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

Gnomad4 AFR AF: 0.470

Gnomad4 AMR AF: 0.704

Gnomad4 ASJ AF: 0.651

Gnomad4 EAS AF: 0.898

Gnomad4 SAS AF: 0.755

Gnomad4 FIN AF: 0.524

Gnomad4 NFE AF: 0.650

Gnomad4 OTH AF: 0.647

Alfa AF: 0.643 Hom.: 29156

Bravo AF: 0.619

Asia WGS AF: 0.830 AC: 2885 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6863418; hg19: chr5-173625154;