rs6897549

Variant names:

• chr5-174205895-G-C
• rs6897549
• ENST00000521585.5:c.*18+591G>C

Your query was ambiguous. Multiple possible variants found:

• chr5-174205895-G-C
• chr5-174205895-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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=-0.88).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NSG2	ENST00000521585.5	c.*18+591G>C		intron_variant	Intron 4 of 4	4		ENSP00000429863.1

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

African (AFR) AF: 0.483 AC: 20016 AN: 41436

American (AMR) AF: 0.516 AC: 7885 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.360 AC: 1249 AN: 3470

East Asian (EAS) AF: 0.738 AC: 3816 AN: 5172

South Asian (SAS) AF: 0.512 AC: 2466 AN: 4812

European-Finnish (FIN) AF: 0.279 AC: 2958 AN: 10586

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.339 AC: 23064 AN: 67980

Other (OTH) AF: 0.414 AC: 875 AN: 2112

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
PhyloP100		0.56
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: rs6897549; hg19: chr5-173632898;