chr5-174144674-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000521585.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NSG2	ENST00000521585.5	TSL:4	c.214-60526G>A		intron	N/A	ENSP00000429863.1	E5RH73

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

African (AFR) AF: 0.154 AC: 6401 AN: 41514

American (AMR) AF: 0.463 AC: 7067 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 1001 AN: 3472

East Asian (EAS) AF: 0.937 AC: 4843 AN: 5168

South Asian (SAS) AF: 0.481 AC: 2315 AN: 4812

European-Finnish (FIN) AF: 0.374 AC: 3957 AN: 10568

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.321 AC: 21809 AN: 67950

Other (OTH) AF: 0.316 AC: 669 AN: 2114

Alfa AF: 0.325 Hom.: 14521

Bravo AF: 0.321

Asia WGS AF: 0.634 AC: 2202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.53
PhyloP100		0.17
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs6556114; hg19: chr5-173571677;