Variant 8-94378693-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.2248-59G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 1,144,010 control chromosomes in the GnomAD database, including 87,330 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.40 ( 12471 hom., cov: 32)

Exomes 𝑓: 0.38 ( 74859 hom. )

Consequence

RAD54B
NM_012415.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 1.11

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:

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 8-94378693-C-T is Benign according to our data. Variant chr8-94378693-C-T is described in ClinVar as [Benign]. Clinvar id is 1252579.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.501 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.2248-59G>A		intron_variant		ENST00000336148.10	NP_036547.1	Q9Y620-1
RAD54B	NM_001205263.2 linkuse as main transcript	c.1696-59G>A		intron_variant			NP_001192192.1	Q9Y620

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RAD54B	ENST00000336148.10 linkuse as main transcript	c.2248-59G>A		intron_variant		1	NM_012415.3	ENSP00000336606.5		Q9Y620-1
FSBP	ENST00000517506.2 linkuse as main transcript	n.*1928-59G>A		intron_variant		5		ENSP00000462684.1		J3KSW4

Frequencies

GnomAD3 genomes

AF:

0.403

AC:

61160

AN:

151860

Hom.:

12462

Cov.:

show subpopulations

Gnomad AFR

AF:

0.404

Gnomad AMI

AF:

0.312

Gnomad AMR

AF:

0.510

Gnomad ASJ

AF:

0.393

Gnomad EAS

AF:

0.467

Gnomad SAS

AF:

0.424

Gnomad FIN

AF:

0.410

Gnomad MID

AF:

0.430

Gnomad NFE

AF:

0.371

Gnomad OTH

AF:

0.434

GnomAD4 exome

AF:

0.383

AC:

380127

AN:

992032

Hom.:

74859

AF XY:

0.384

AC XY:

195443

AN XY:

509444

show subpopulations

Gnomad4 AFR exome

AF:

0.417

Gnomad4 AMR exome

AF:

0.577

Gnomad4 ASJ exome

AF:

0.398

Gnomad4 EAS exome

AF:

0.467

Gnomad4 SAS exome

AF:

0.416

Gnomad4 FIN exome

AF:

0.420

Gnomad4 NFE exome

AF:

0.363

Gnomad4 OTH exome

AF:

0.386

GnomAD4 genome

AF:

0.403

AC:

61205

AN:

151978

Hom.:

12471

Cov.:

AF XY:

0.409

AC XY:

30404

AN XY:

74282

show subpopulations

Gnomad4 AFR

AF:

0.404

Gnomad4 AMR

AF:

0.510

Gnomad4 ASJ

AF:

0.393

Gnomad4 EAS

AF:

0.467

Gnomad4 SAS

AF:

0.423

Gnomad4 FIN

AF:

0.410

Gnomad4 NFE

AF:

0.371

Gnomad4 OTH

AF:

0.431

Alfa

AF:

0.388

Hom.:

2327

Bravo

AF:

0.412

Asia WGS

AF:

0.421

AC:

1465

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

-0.92

CADD

Benign

1.3

DANN

Benign

0.24

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