Variant rs5994562 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_014306.5(RTCB):c.1410+151A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.558 in 688,980 control chromosomes in the GnomAD database, including 110,854 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 0.62 ( 30653 hom., cov: 32)

Exomes 𝑓: 0.54 ( 80201 hom. )

Consequence

RTCB
NM_014306.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.72

Variant links:

Genes affected

RTCB (HGNC:26935): (RNA 2',3'-cyclic phosphate and 5'-OH ligase) Enables RNA ligase (ATP) activity and vinculin binding activity. Involved in tRNA splicing, via endonucleolytic cleavage and ligation. Located in cytosol and nucleoplasm. Part of tRNA-splicing ligase complex. [provided by Alliance of Genome Resources, Apr 2022]

RTCB 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=-0.96).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RTCB	NM_014306.5 linkuse as main transcript	c.1410+151A>T		intron_variant		ENST00000216038.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RTCB	ENST00000216038.6 linkuse as main transcript	c.1410+151A>T		intron_variant		1	NM_014306.5	P1

Frequencies

GnomAD3 genomes

AF:

0.621

AC:

94240

AN:

151806

Hom.:

30615

Cov.:

show subpopulations

Gnomad AFR

AF:

0.843

Gnomad AMI

AF:

0.665

Gnomad AMR

AF:

0.573

Gnomad ASJ

AF:

0.447

Gnomad EAS

AF:

0.559

Gnomad SAS

AF:

0.523

Gnomad FIN

AF:

0.513

Gnomad MID

AF:

0.564

Gnomad NFE

AF:

0.534

Gnomad OTH

AF:

0.572

GnomAD4 exome

AF:

0.541

AC:

290290

AN:

537056

Hom.:

80201

AF XY:

0.536

AC XY:

148550

AN XY:

277016

show subpopulations

Gnomad4 AFR exome

AF:

0.851

Gnomad4 AMR exome

AF:

0.556

Gnomad4 ASJ exome

AF:

0.442

Gnomad4 EAS exome

AF:

0.540

Gnomad4 SAS exome

AF:

0.518

Gnomad4 FIN exome

AF:

0.522

Gnomad4 NFE exome

AF:

0.535

Gnomad4 OTH exome

AF:

0.547

GnomAD4 genome

AF:

0.621

AC:

94341

AN:

151924

Hom.:

30653

Cov.:

AF XY:

0.617

AC XY:

45818

AN XY:

74236

show subpopulations

Gnomad4 AFR

AF:

0.843

Gnomad4 AMR

AF:

0.574

Gnomad4 ASJ

AF:

0.447

Gnomad4 EAS

AF:

0.558

Gnomad4 SAS

AF:

0.521

Gnomad4 FIN

AF:

0.513

Gnomad4 NFE

AF:

0.534

Gnomad4 OTH

AF:

0.575

Alfa

AF:

0.583

Hom.:

3367

Bravo

AF:

0.634

Asia WGS

AF:

0.566

AC:

1968

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.52

DANN

Benign

0.18

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over