Variant 5-74767329-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_014886.6(NSA2):c.-32C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 1,611,832 control chromosomes in the GnomAD database, including 53,886 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.32 ( 9884 hom., cov: 32)

Exomes 𝑓: 0.24 ( 44002 hom. )

Consequence

NSA2
NM_014886.6 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.22

Variant links:

Genes affected

NSA2 (HGNC:30728): (NSA2 ribosome biogenesis factor) This gene encodes a nucleolar protein involved in cell cycle regulation and proliferation. This gene was identified based on sequence similarity to a highly conserved Saccharomyces cerevisiae gene encoding a pre-ribosomal protein, which is involved in large ribosomal subunit biogenesis. The encoded protein is found at elevated levels in diabetic nephropathy. Alternative splicing results in multiple transcript variants. Several related pseudogenes have been identified. [provided by RefSeq, Nov 2012]

NSA2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.02).

BP6

Variant 5-74767329-C-G is Benign according to our data. Variant chr5-74767329-C-G is described in ClinVar as [Benign]. Clinvar id is 1276589.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NSA2	NM_014886.6 linkuse as main transcript	c.-32C>G		5_prime_UTR_variant	1/6	ENST00000610426.5

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris
NSA2	ENST00000610426.5 linkuse as main transcript	c.-32C>G	5_prime_UTR_variant	1/6	1	NM_014886.6	P1
NSA2	ENST00000296802.9 linkuse as main transcript	c.-32C>G	5_prime_UTR_variant	1/5	5
NSA2	ENST00000513356.1 linkuse as main transcript	n.67C>G	non_coding_transcript_exon_variant	1/5	3
NSA2	ENST00000514918.5 linkuse as main transcript	n.82C>G	non_coding_transcript_exon_variant	1/3	2

Frequencies

GnomAD3 genomes

AF:

0.325

AC:

49325

AN:

151956

Hom.:

9855

Cov.:

show subpopulations

Gnomad AFR

AF:

0.564

Gnomad AMI

AF:

0.149

Gnomad AMR

AF:

0.340

Gnomad ASJ

AF:

0.258

Gnomad EAS

AF:

0.203

Gnomad SAS

AF:

0.236

Gnomad FIN

AF:

0.157

Gnomad MID

AF:

0.364

Gnomad NFE

AF:

0.222

Gnomad OTH

AF:

0.332

GnomAD3 exomes

AF:

0.260

AC:

65155

AN:

250648

Hom.:

9680

AF XY:

0.251

AC XY:

34087

AN XY:

135660

show subpopulations

Gnomad AFR exome

AF:

0.576

Gnomad AMR exome

AF:

0.351

Gnomad ASJ exome

AF:

0.279

Gnomad EAS exome

AF:

0.206

Gnomad SAS exome

AF:

0.228

Gnomad FIN exome

AF:

0.165

Gnomad NFE exome

AF:

0.221

Gnomad OTH exome

AF:

0.262

GnomAD4 exome

AF:

0.236

AC:

344801

AN:

1459758

Hom.:

44002

Cov.:

AF XY:

0.235

AC XY:

170576

AN XY:

726150

show subpopulations

Gnomad4 AFR exome

AF:

0.585

Gnomad4 AMR exome

AF:

0.349

Gnomad4 ASJ exome

AF:

0.276

Gnomad4 EAS exome

AF:

0.184

Gnomad4 SAS exome

AF:

0.228

Gnomad4 FIN exome

AF:

0.168

Gnomad4 NFE exome

AF:

0.224

Gnomad4 OTH exome

AF:

0.262

GnomAD4 genome

AF:

0.325

AC:

49408

AN:

152074

Hom.:

9884

Cov.:

AF XY:

0.321

AC XY:

23854

AN XY:

74352

show subpopulations

Gnomad4 AFR

AF:

0.565

Gnomad4 AMR

AF:

0.340

Gnomad4 ASJ

AF:

0.258

Gnomad4 EAS

AF:

0.203

Gnomad4 SAS

AF:

0.235

Gnomad4 FIN

AF:

0.157

Gnomad4 NFE

AF:

0.222

Gnomad4 OTH

AF:

0.328

Alfa

AF:

0.192

Hom.:

601

Bravo

AF:

0.353

Asia WGS

AF:

0.263

AC:

915

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 29, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

5.0

DANN

Benign

0.47

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over