rs6556114

Variant names:

• chr5-174144674-G-A
• rs6556114
• ENST00000521585.5:c.214-60526G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-174144674-G-A
• chr5-174144674-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NSG2	ENST00000521585.5	c.214-60526G>A		intron_variant	Intron 3 of 4	4		ENSP00000429863.1

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;