Variant 8-94387390-C-T 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_012415.3(RAD54B):c.1810-231G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 345,126 control chromosomes in the GnomAD database, including 26,438 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.39 ( 11521 hom., cov: 32)

Exomes 𝑓: 0.39 ( 14917 hom. )

Consequence

RAD54B
NM_012415.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.0400

Variant links:

Genes affected

RAD54B (HGNC:17228): (RAD54 homolog B) The protein encoded by this gene belongs to the DEAD-like helicase superfamily. It shares similarity with Saccharomyces cerevisiae RAD54 and RDH54, both of which are involved in homologous recombination and repair of DNA. This protein binds to double-stranded DNA, and displays ATPase activity in the presence of DNA. This gene is highly expressed in testis and spleen, which suggests active roles in meiotic and mitotic recombination. Homozygous mutations of this gene were observed in primary lymphoma and colon cancer. [provided by RefSeq, Jul 2008]

RAD54B links:

RAD54B (HGNC:):

RAD54B links:

FSBP (HGNC:43653): (fibrinogen silencer binding protein) Enables identical protein binding activity. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

FSBP 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=-0.88).

BP6

Variant 8-94387390-C-T is Benign according to our data. Variant chr8-94387390-C-T is described in ClinVar as [Benign]. Clinvar id is 1290502.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RAD54B	NM_012415.3 linkuse as main transcript	c.1810-231G>A		intron_variant		ENST00000336148.10	NP_036547.1	Q9Y620-1
RAD54B	NM_001205263.2 linkuse as main transcript	c.1258-231G>A		intron_variant			NP_001192192.1	Q9Y620

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
RAD54B	ENST00000336148.10 linkuse as main transcript	c.1810-231G>A	intron_variant		1	NM_012415.3	ENSP00000336606.5	Q9Y620-1
RAD54B	ENST00000518358.1 linkuse as main transcript	n.40G>A	non_coding_transcript_exon_variant	1/2	3
FSBP	ENST00000517506.2 linkuse as main transcript	n.*1490-231G>A	intron_variant		5		ENSP00000462684.1	J3KSW4

Frequencies

GnomAD3 genomes

AF:

0.387

AC:

58720

AN:

151848

Hom.:

11518

Cov.:

show subpopulations

Gnomad AFR

AF:

0.348

Gnomad AMI

AF:

0.312

Gnomad AMR

AF:

0.502

Gnomad ASJ

AF:

0.386

Gnomad EAS

AF:

0.468

Gnomad SAS

AF:

0.424

Gnomad FIN

AF:

0.410

Gnomad MID

AF:

0.424

Gnomad NFE

AF:

0.372

Gnomad OTH

AF:

0.418

GnomAD4 exome

AF:

0.390

AC:

75412

AN:

193160

Hom.:

14917

Cov.:

AF XY:

0.391

AC XY:

38597

AN XY:

98796

show subpopulations

Gnomad4 AFR exome

AF:

0.369

Gnomad4 AMR exome

AF:

0.533

Gnomad4 ASJ exome

AF:

0.390

Gnomad4 EAS exome

AF:

0.473

Gnomad4 SAS exome

AF:

0.386

Gnomad4 FIN exome

AF:

0.430

Gnomad4 NFE exome

AF:

0.369

Gnomad4 OTH exome

AF:

0.387

GnomAD4 genome

AF:

0.387

AC:

58755

AN:

151966

Hom.:

11521

Cov.:

AF XY:

0.393

AC XY:

29210

AN XY:

74264

show subpopulations

Gnomad4 AFR

AF:

0.348

Gnomad4 AMR

AF:

0.502

Gnomad4 ASJ

AF:

0.386

Gnomad4 EAS

AF:

0.468

Gnomad4 SAS

AF:

0.423

Gnomad4 FIN

AF:

0.410

Gnomad4 NFE

AF:

0.372

Gnomad4 OTH

AF:

0.414

Alfa

AF:

0.384

Hom.:

1858

Bravo

AF:

0.393

Asia WGS

AF:

0.420

AC:

1461

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	Nov 12, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

2.6

DANN

Benign

0.77

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