rs9882601

Variant names:

• chr3-51583465-A-G
• rs9882601
• NM_015106.4:c.-54-6902A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015106.4(RAD54L2):​c.-54-6902A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0387 in 150,258 control chromosomes in the GnomAD database, including 397 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 0.039 (397 hom., cov: 31)
• Consequence: RAD54L2 NM_015106.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80
• Publications: 1 publications found

Genes affected

RAD54L2 (HGNC:29123): (RAD54 like 2) Predicted to enable ATP hydrolysis activity; protein kinase binding activity; and transcription coregulator activity. Predicted to be involved in DNA duplex unwinding. Predicted to act upstream of or within positive regulation of transcription by RNA polymerase II. Predicted to be located in nuclear speck. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAD54L2	NM_015106.4	c.-54-6902A>G		intron_variant	Intron 2 of 22	ENST00000684192.1	NP_055921.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAD54L2	ENST00000684192.1	c.-54-6902A>G		intron_variant	Intron 2 of 22		NM_015106.4	ENSP00000507587.1
RAD54L2	ENST00000409535.6	c.-54-6902A>G		intron_variant	Intron 1 of 21	5		ENSP00000386520.1
RAD54L2	ENST00000487093.5	n.72-6902A>G		intron_variant	Intron 1 of 21	5

Frequencies

GnomAD3 genomes AF: 0.0387 AC: 5814 AN: 150158 Hom.: 396 Cov.: 31

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0179

Gnomad ASJ AF: 0.0104

Gnomad EAS AF: 0.00254

Gnomad SAS AF: 0.00504

Gnomad FIN AF: 0.00310

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.000783

Gnomad OTH AF: 0.0228

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

GnomAD4 genome AF: 0.0387 AC: 5822 AN: 150258 Hom.: 397 Cov.: 31 AF XY: 0.0371 AC XY: 2717 AN XY: 73216

African (AFR) AF: 0.131 AC: 5347 AN: 40888

American (AMR) AF: 0.0179 AC: 269 AN: 15070

Ashkenazi Jewish (ASJ) AF: 0.0104 AC: 36 AN: 3454

East Asian (EAS) AF: 0.00254 AC: 13 AN: 5114

South Asian (SAS) AF: 0.00505 AC: 24 AN: 4748

European-Finnish (FIN) AF: 0.00310 AC: 31 AN: 10006

Middle Eastern (MID) AF: 0.00685 AC: 2 AN: 292

European-Non Finnish (NFE) AF: 0.000783 AC: 53 AN: 67704

Other (OTH) AF: 0.0226 AC: 47 AN: 2080

Alfa AF: 0.0264 Hom.: 39

Bravo AF: 0.0435

Asia WGS AF: 0.0100 AC: 36 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.63
PhyloP100		-1.8
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9882601; hg19: chr3-51617481;