Genetic Variant NSG2:c.*369A>T (chr5-174107874-A-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_015980.5(NSG2):c.*369A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

NSG2
NM_015980.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.796

Publications

10 publications found

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 was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NSG2	NM_015980.5 link	c.*369A>T		3_prime_UTR_variant	Exon 5 of 5	ENST00000303177.8	NP_057064.1	Q9Y328

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
NSG2	ENST00000303177.8 link	c.*369A>T	3_prime_UTR_variant	Exon 5 of 5	1	NM_015980.5	ENSP00000307722.3	Q9Y328
NSG2	ENST00000521146.1 link	n.786A>T	non_coding_transcript_exon_variant	Exon 3 of 3	2
NSG2	ENST00000521959.5 link	n.830A>T	non_coding_transcript_exon_variant	Exon 4 of 4	2
NSG2	ENST00000521585.5 link	c.213+43559A>T	intron_variant	Intron 3 of 4	4		ENSP00000429863.1	E5RH73

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

249666

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

139444

African (AFR)

AF:

0.00

AC:

AN:

6756

American (AMR)

AF:

0.00

AC:

AN:

18934

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

6598

East Asian (EAS)

AF:

0.00

AC:

AN:

9706

South Asian (SAS)

AF:

0.00

AC:

AN:

47008

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10340

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1928

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

136280

Other (OTH)

AF:

0.00

AC:

AN:

12116

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

2.6

(source)

DANN

Benign

0.62

PhyloP100

0.80

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over