Variant 20-2462470-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_003091.4(SNRPB):c.685+166C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 719,330 control chromosomes in the GnomAD database, including 9,164 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.17 ( 2423 hom., cov: 33)

Exomes 𝑓: 0.14 ( 6741 hom. )

Consequence

SNRPB
NM_003091.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.152

Variant links:

Genes affected

SNRPB (HGNC:11153): (small nuclear ribonucleoprotein polypeptides B and B1) The protein encoded by this gene is one of several nuclear proteins that are found in common among U1, U2, U4/U6, and U5 small ribonucleoprotein particles (snRNPs). These snRNPs are involved in pre-mRNA splicing, and the encoded protein may also play a role in pre-mRNA splicing or snRNP structure. Autoantibodies from patients with systemic lupus erythematosus frequently recognize epitopes on the encoded protein. Two transcript variants encoding different isoforms (B and B') have been found for this gene. [provided by RefSeq, Jul 2008]

SNRPB links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 20-2462470-G-A is Benign according to our data. Variant chr20-2462470-G-A is described in ClinVar as [Benign]. Clinvar id is 1248360.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SNRPB	NM_003091.4 linkuse as main transcript	c.685+166C>T		intron_variant		ENST00000381342.7	NP_003082.1
SNRPB	NM_198216.2 linkuse as main transcript	c.685+166C>T		intron_variant			NP_937859.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SNRPB	ENST00000381342.7 linkuse as main transcript	c.685+166C>T		intron_variant		1	NM_003091.4	ENSP00000370746	P1	P14678-2

Frequencies

GnomAD3 genomes

AF:

0.168

AC:

25608

AN:

152078

Hom.:

2420

Cov.:

show subpopulations

Gnomad AFR

AF:

0.239

Gnomad AMI

AF:

0.0735

Gnomad AMR

AF:

0.170

Gnomad ASJ

AF:

0.113

Gnomad EAS

AF:

0.261

Gnomad SAS

AF:

0.199

Gnomad FIN

AF:

0.179

Gnomad MID

AF:

0.120

Gnomad NFE

AF:

0.118

Gnomad OTH

AF:

0.159

GnomAD4 exome

AF:

0.144

AC:

81740

AN:

567134

Hom.:

6741

AF XY:

0.144

AC XY:

43764

AN XY:

304076

show subpopulations

Gnomad4 AFR exome

AF:

0.232

Gnomad4 AMR exome

AF:

0.206

Gnomad4 ASJ exome

AF:

0.124

Gnomad4 EAS exome

AF:

0.244

Gnomad4 SAS exome

AF:

0.177

Gnomad4 FIN exome

AF:

0.169

Gnomad4 NFE exome

AF:

0.117

Gnomad4 OTH exome

AF:

0.142

GnomAD4 genome

AF:

0.168

AC:

25624

AN:

152196

Hom.:

2423

Cov.:

AF XY:

0.171

AC XY:

12736

AN XY:

74416

show subpopulations

Gnomad4 AFR

AF:

0.239

Gnomad4 AMR

AF:

0.170

Gnomad4 ASJ

AF:

0.113

Gnomad4 EAS

AF:

0.262

Gnomad4 SAS

AF:

0.198

Gnomad4 FIN

AF:

0.179

Gnomad4 NFE

AF:

0.118

Gnomad4 OTH

AF:

0.164

Alfa

AF:

0.142

Hom.:

389

Bravo

AF:

0.172

Asia WGS

AF:

0.244

AC:

844

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 16, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

4.5

DANN

Benign

0.46

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over