rs9882601

Positions:

• chr3-51583465-A-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
RAD54L2	NM_015106.4	c.-54-6902A>G		intron_variant		ENST00000684192.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RAD54L2	ENST00000684192.1	c.-54-6902A>G		intron_variant			NM_015106.4	P1
RAD54L2	ENST00000409535.6	c.-54-6902A>G		intron_variant		5		P1
RAD54L2	ENST00000487093.5	n.72-6902A>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.0179

Gnomad4 ASJ AF: 0.0104

Gnomad4 EAS AF: 0.00254

Gnomad4 SAS AF: 0.00505

Gnomad4 FIN AF: 0.00310

Gnomad4 NFE AF: 0.000783

Gnomad4 OTH AF: 0.0226

Alfa AF: 0.0225 Hom.: 35

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

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: rs9882601; hg19: chr3-51617481;