rs6556114

chr5-174144674-G-Achr5-174144674-G-C

Variant summary

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

The ENST00000521585.5(NSG2):c.214-60526G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 152,082 control chromosomes in the GnomAD database, including 9,744 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 0.32 (9744 hom., cov: 32)
• Consequence: NSG2 ENST00000521585.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.174

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NSG2	ENST00000521585.5	c.214-60526G>A		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48420 AN: 151964 Hom.: 9743 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.318 AC: 48437 AN: 152082 Hom.: 9744 Cov.: 32 AF XY: 0.331 AC XY: 24636 AN XY: 74338

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.288

Gnomad4 EAS AF: 0.937

Gnomad4 SAS AF: 0.481

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.321

Gnomad4 OTH AF: 0.316

Alfa AF: 0.328 Hom.: 11785

Bravo AF: 0.321

Asia WGS AF: 0.634 AC: 2202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.6
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6556114; hg19: chr5-173571677;