rs6897549

chr5-174205895-G-Cchr5-174205895-G-T

Variant summary

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

The ENST00000521585.5(NSG2):c.*18+591G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 152,050 control chromosomes in the GnomAD database, including 13,808 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 0.41 (13808 hom., cov: 32)
• Consequence: NSG2 ENST00000521585.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.565

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.718 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.*18+591G>C		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62765 AN: 151932 Hom.: 13785 Cov.: 32

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.413 AC: 62837 AN: 152050 Hom.: 13808 Cov.: 32 AF XY: 0.417 AC XY: 31012 AN XY: 74300

Gnomad4 AFR AF: 0.483

Gnomad4 AMR AF: 0.516

Gnomad4 ASJ AF: 0.360

Gnomad4 EAS AF: 0.738

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.279

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.414

Alfa AF: 0.377 Hom.: 1403

Bravo AF: 0.435

Asia WGS AF: 0.617 AC: 2142 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	8.3
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6897549; hg19: chr5-173632898;