Variant 6-52995577-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_001445.2(RN7SK):n.-43C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 165,814 control chromosomes in the GnomAD database, including 5,852 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 0.26 ( 5497 hom., cov: 33)

Exomes 𝑓: 0.22 ( 355 hom. )

Consequence

RN7SK
NR_001445.2 upstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -5.78

Variant links:

Genes affected

7SK (HGNC:):

7SK links:

RN7SK (HGNC:10037): (RNA component of 7SK nuclear ribonucleoprotein)

RN7SK links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RN7SK	NR_001445.2 link	n.-43C>T		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
7SK	ENST00000365328.1 link	n.-43C>T		upstream_gene_variant		6
RN7SK	ENST00000636484.1 link	n.-44C>T		upstream_gene_variant		6

Frequencies

GnomAD3 genomes

AF:

0.262

AC:

39721

AN:

151838

Hom.:

5477

Cov.:

show subpopulations

Gnomad AFR

AF:

0.341

Gnomad AMI

AF:

0.186

Gnomad AMR

AF:

0.219

Gnomad ASJ

AF:

0.314

Gnomad EAS

AF:

0.132

Gnomad SAS

AF:

0.158

Gnomad FIN

AF:

0.207

Gnomad MID

AF:

0.310

Gnomad NFE

AF:

0.247

Gnomad OTH

AF:

0.256

GnomAD4 exome

AF:

0.219

AC:

3029

AN:

13858

Hom.:

355

Cov.:

AF XY:

0.219

AC XY:

1427

AN XY:

6502

show subpopulations

Gnomad4 AFR exome

AF:

0.331

Gnomad4 AMR exome

AF:

0.190

Gnomad4 ASJ exome

AF:

0.262

Gnomad4 EAS exome

AF:

0.139

Gnomad4 SAS exome

AF:

0.113

Gnomad4 FIN exome

AF:

0.224

Gnomad4 NFE exome

AF:

0.239

Gnomad4 OTH exome

AF:

0.228

GnomAD4 genome

AF:

0.262

AC:

39772

AN:

151956

Hom.:

5497

Cov.:

AF XY:

0.256

AC XY:

19043

AN XY:

74278

show subpopulations

Gnomad4 AFR

AF:

0.342

Gnomad4 AMR

AF:

0.219

Gnomad4 ASJ

AF:

0.314

Gnomad4 EAS

AF:

0.132

Gnomad4 SAS

AF:

0.157

Gnomad4 FIN

AF:

0.207

Gnomad4 NFE

AF:

0.247

Gnomad4 OTH

AF:

0.253

Alfa

AF:

0.168

Hom.:

769

Bravo

AF:

0.267

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

0.0010

DANN

Benign

0.74

Splicing

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