Variant rs4148727 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001134405.2(RUNDC3B):c.458+2795A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0485 in 152,192 control chromosomes in the GnomAD database, including 270 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as drug response (no stars).

Frequency

Genomes: 𝑓 0.048 ( 270 hom., cov: 32)

Exomes 𝑓: 0.063 ( 0 hom. )

Consequence

RUNDC3B
NM_001134405.2 intron

Scores

Clinical Significance

drug response no assertion criteria provided O:1

Conservation

PhyloP100: 0.0550

Variant links:

Genes affected

RUNDC3B (HGNC:30286): (RUN domain containing 3B)

RUNDC3B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0898 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RUNDC3B	NM_001134405.2 link	c.458+2795A>G		intron_variant		ENST00000394654.4	NP_001127877.1	Q96NL0-5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RUNDC3B	ENST00000394654.4 link	c.458+2795A>G		intron_variant		2	NM_001134405.2	ENSP00000378149.3		Q96NL0-5

Frequencies

GnomAD3 genomes

AF:

0.0485

AC:

7379

AN:

152058

Hom.:

270

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0806

Gnomad AMI

AF:

0.0592

Gnomad AMR

AF:

0.0568

Gnomad ASJ

AF:

0.0392

Gnomad EAS

AF:

0.0973

Gnomad SAS

AF:

0.0358

Gnomad FIN

AF:

0.0369

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.0265

Gnomad OTH

AF:

0.0522

GnomAD4 exome

AF:

0.0625

AC:

AN:

Hom.:

AF XY:

0.0833

AC XY:

AN XY:

show subpopulations

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.100

GnomAD4 genome

AF:

0.0485

AC:

7377

AN:

152176

Hom.:

270

Cov.:

AF XY:

0.0490

AC XY:

3643

AN XY:

74402

show subpopulations

Gnomad4 AFR

AF:

0.0805

Gnomad4 AMR

AF:

0.0567

Gnomad4 ASJ

AF:

0.0392

Gnomad4 EAS

AF:

0.0968

Gnomad4 SAS

AF:

0.0354

Gnomad4 FIN

AF:

0.0369

Gnomad4 NFE

AF:

0.0265

Gnomad4 OTH

AF:

0.0511

Alfa

AF:

0.0343

Hom.:

Bravo

AF:

0.0532

Asia WGS

AF:

0.0600

AC:

207

AN:

3478

ClinVar

Significance: drug response

Submissions summary: Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Tramadol response

Other:1

drug response, no assertion criteria provided

research

Bruce Budowle Laboratory, University of North Texas Health Science Center

Apr 28, 2018

- T:M1 = postmortem ratio or tramadol to O-desmethyltramadol; t-MP = model-based clustered metabolizer phenotype inferred from T:M1

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.64

DANN

Benign

0.65

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