Variant rs1130329 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001204513.3(RBAK-RBAKDN):c.*34A>C variant causes a splice region, 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 1,608,512 control chromosomes in the GnomAD database, including 91,144 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.36 ( 10161 hom., cov: 32)

Exomes 𝑓: 0.33 ( 80983 hom. )

Consequence

RBAK-RBAKDN
NM_001204513.3 splice_region, 3_prime_UTR

Scores

Splicing: ADA: 0.0009329

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0960

Variant links:

Genes affected

RBAK-RBAKDN (HGNC:):

RBAK-RBAKDN links:

RBAKDN (HGNC:33770): (RBAK downstream neighbor)

RBAKDN 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 (MetaRNN=2.2622943E-4).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RBAK-RBAKDN	NM_001204513.3 linkuse as main transcript	c.*34A>C		splice_region_variant, 3_prime_UTR_variant	6/6		NP_001191442.1
RBAKDN	NR_015343.2 linkuse as main transcript	n.279A>C		splice_region_variant, non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RBAKDN	ENST00000498308.1 linkuse as main transcript	n.214A>C		splice_region_variant, non_coding_transcript_exon_variant	3/3	1

Frequencies

GnomAD3 genomes

AF:

0.359

AC:

54512

AN:

151950

Hom.:

10149

Cov.:

show subpopulations

Gnomad AFR

AF:

0.437

Gnomad AMI

AF:

0.193

Gnomad AMR

AF:

0.284

Gnomad ASJ

AF:

0.389

Gnomad EAS

AF:

0.329

Gnomad SAS

AF:

0.457

Gnomad FIN

AF:

0.364

Gnomad MID

AF:

0.453

Gnomad NFE

AF:

0.322

Gnomad OTH

AF:

0.366

GnomAD3 exomes

AF:

0.346

AC:

84731

AN:

245176

Hom.:

15143

AF XY:

0.352

AC XY:

46866

AN XY:

132978

show subpopulations

Gnomad AFR exome

AF:

0.435

Gnomad AMR exome

AF:

0.264

Gnomad ASJ exome

AF:

0.386

Gnomad EAS exome

AF:

0.338

Gnomad SAS exome

AF:

0.454

Gnomad FIN exome

AF:

0.355

Gnomad NFE exome

AF:

0.324

Gnomad OTH exome

AF:

0.356

GnomAD4 exome

AF:

0.329

AC:

479303

AN:

1456444

Hom.:

80983

Cov.:

AF XY:

0.333

AC XY:

241407

AN XY:

724018

show subpopulations

Gnomad4 AFR exome

AF:

0.440

Gnomad4 AMR exome

AF:

0.263

Gnomad4 ASJ exome

AF:

0.386

Gnomad4 EAS exome

AF:

0.353

Gnomad4 SAS exome

AF:

0.458

Gnomad4 FIN exome

AF:

0.354

Gnomad4 NFE exome

AF:

0.314

Gnomad4 OTH exome

AF:

0.348

GnomAD4 genome

AF:

0.359

AC:

54562

AN:

152068

Hom.:

10161

Cov.:

AF XY:

0.360

AC XY:

26750

AN XY:

74332

show subpopulations

Gnomad4 AFR

AF:

0.437

Gnomad4 AMR

AF:

0.283

Gnomad4 ASJ

AF:

0.389

Gnomad4 EAS

AF:

0.330

Gnomad4 SAS

AF:

0.458

Gnomad4 FIN

AF:

0.364

Gnomad4 NFE

AF:

0.322

Gnomad4 OTH

AF:

0.369

Alfa

AF:

0.336

Hom.:

18470

Bravo

AF:

0.355

TwinsUK

AF:

0.319

AC:

1182

ALSPAC

AF:

0.321

AC:

1239

ESP6500AA

AF:

0.427

AC:

1881

ESP6500EA

AF:

0.326

AC:

2805

ExAC

AF:

0.349

AC:

42391

Asia WGS

AF:

0.383

AC:

1329

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.70

BayesDel_noAF

Benign

-0.63

CADD

Benign

1.2

DANN

Benign

0.95

Eigen

Benign

-0.45

Eigen_PC

Benign

-0.71

FATHMM_MKL

Benign

0.027

LIST_S2

Benign

0.26

MetaRNN

Benign

0.00023

MetaSVM

Benign

-0.99

PROVEAN

Benign

-1.4

REVEL

Benign

0.015

Sift

Benign

0.27

Sift4G

Benign

0.097

Vest4

0.039

ClinPred

0.0023

GERP RS

0.45

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00093

dbscSNV1_RF

Benign

0.028

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