rs2921385

Variant names:

• chr8-94447120-T-C
• rs2921385
• NM_012415.3:c.304+11148A>G

Your query was ambiguous. Multiple possible variants found:

• chr8-94447120-T-C
• chr8-94447120-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012415.3(RAD54B):​c.304+11148A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.564 in 151,970 control chromosomes in the GnomAD database, including 26,330 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 0.56 (26330 hom., cov: 32)
• Consequence: RAD54B NM_012415.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.846

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAD54B	NM_012415.3	c.304+11148A>G		intron_variant	Intron 3 of 14	ENST00000336148.10	NP_036547.1
RAD54B	NM_001205262.3	c.304+11148A>G		intron_variant	Intron 3 of 3		NP_001192191.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAD54B	ENST00000336148.10	c.304+11148A>G		intron_variant	Intron 3 of 14	1	NM_012415.3	ENSP00000336606.5

Frequencies

GnomAD3 genomes AF: 0.564 AC: 85648 AN: 151852 Hom.: 26282 Cov.: 32

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.821

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.559

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.564 AC: 85761 AN: 151970 Hom.: 26330 Cov.: 32 AF XY: 0.570 AC XY: 42364 AN XY: 74292

Gnomad4 AFR AF: 0.786

Gnomad4 AMR AF: 0.608

Gnomad4 ASJ AF: 0.448

Gnomad4 EAS AF: 0.820

Gnomad4 SAS AF: 0.595

Gnomad4 FIN AF: 0.473

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.565

Alfa AF: 0.542 Hom.: 4536

Bravo AF: 0.585

Asia WGS AF: 0.711 AC: 2471 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	8.7
DANN	Benign	0.90

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

Other links and lift over

dbSNP: rs2921385; hg19: chr8-95459348;