5-174198151-T-C

Position:

• chr5-174198151-T-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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NSG2	ENST00000521585.5	c.214-7049T>C		intron_variant		4		ENSP00000429863

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;