Variant rs4457100 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015980.5(NSG2):c.*369A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 401,606 control chromosomes in the GnomAD database, including 19,268 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 0.34 ( 11674 hom., cov: 32)

Exomes 𝑓: 0.23 ( 7594 hom. )

Consequence

NSG2
NM_015980.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.796

Variant links:

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]

NSG2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.641 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NSG2	NM_015980.5 linkuse as main transcript	c.*369A>G		3_prime_UTR_variant	5/5	ENST00000303177.8	NP_057064.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris
NSG2	ENST00000303177.8 linkuse as main transcript	c.*369A>G	3_prime_UTR_variant	5/5	1	NM_015980.5	ENSP00000307722	P1
NSG2	ENST00000521585.5 linkuse as main transcript	c.213+43559A>G	intron_variant		4		ENSP00000429863
NSG2	ENST00000521146.1 linkuse as main transcript	n.786A>G	non_coding_transcript_exon_variant	3/3	2
NSG2	ENST00000521959.5 linkuse as main transcript	n.830A>G	non_coding_transcript_exon_variant	4/4	2

Frequencies

GnomAD3 genomes

AF:

0.336

AC:

51130

AN:

151964

Hom.:

11633

Cov.:

show subpopulations

Gnomad AFR

AF:

0.648

Gnomad AMI

AF:

0.322

Gnomad AMR

AF:

0.254

Gnomad ASJ

AF:

0.239

Gnomad EAS

AF:

0.0945

Gnomad SAS

AF:

0.246

Gnomad FIN

AF:

0.187

Gnomad MID

AF:

0.253

Gnomad NFE

AF:

0.220

Gnomad OTH

AF:

0.320

GnomAD4 exome

AF:

0.231

AC:

57534

AN:

249524

Hom.:

7594

Cov.:

AF XY:

0.230

AC XY:

32055

AN XY:

139350

show subpopulations

Gnomad4 AFR exome

AF:

0.644

Gnomad4 AMR exome

AF:

0.203

Gnomad4 ASJ exome

AF:

0.238

Gnomad4 EAS exome

AF:

0.0909

Gnomad4 SAS exome

AF:

0.239

Gnomad4 FIN exome

AF:

0.188

Gnomad4 NFE exome

AF:

0.222

Gnomad4 OTH exome

AF:

0.242

GnomAD4 genome

AF:

0.337

AC:

51229

AN:

152082

Hom.:

11674

Cov.:

AF XY:

0.329

AC XY:

24445

AN XY:

74332

show subpopulations

Gnomad4 AFR

AF:

0.648

Gnomad4 AMR

AF:

0.254

Gnomad4 ASJ

AF:

0.239

Gnomad4 EAS

AF:

0.0947

Gnomad4 SAS

AF:

0.246

Gnomad4 FIN

AF:

0.187

Gnomad4 NFE

AF:

0.220

Gnomad4 OTH

AF:

0.325

Alfa

AF:

0.245

Hom.:

8113

Bravo

AF:

0.359

Asia WGS

AF:

0.240

AC:

833

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

3.1

DANN

Benign

0.54

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over