15-40694157-A-G

Position:

• chr15-40694157-A-G

Variant summary

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

The NR_040058.1(RAD51-AS1):​n.733T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.648 in 151,964 control chromosomes in the GnomAD database, including 32,490 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 0.65 (32483 hom., cov: 31)
  • Exomes 𝑓: 0.68 (7 hom.)
• Consequence: RAD51-AS1 NR_040058.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.99

Genes affected

RAD51-AS1 (HGNC:48621): (RAD51 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.904 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RAD51-AS1	NR_040058.1	n.733T>C		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RAD51-AS1	ENST00000526635.2	n.300+429T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.648 AC: 98305 AN: 151810 Hom.: 32425 Cov.: 31

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.926

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.651

Gnomad NFE AF: 0.579

Gnomad OTH AF: 0.621

GnomAD4 exome AF: 0.676 AC: 23 AN: 34 Hom.: 7 Cov.: 0 AF XY: 0.727 AC XY: 16 AN XY: 22

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.679

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.648 AC: 98426 AN: 151930 Hom.: 32483 Cov.: 31 AF XY: 0.657 AC XY: 48797 AN XY: 74262

Gnomad4 AFR AF: 0.691

Gnomad4 AMR AF: 0.686

Gnomad4 ASJ AF: 0.611

Gnomad4 EAS AF: 0.926

Gnomad4 SAS AF: 0.772

Gnomad4 FIN AF: 0.693

Gnomad4 NFE AF: 0.579

Gnomad4 OTH AF: 0.624

Alfa AF: 0.513 Hom.: 1450

Bravo AF: 0.651

Asia WGS AF: 0.846 AC: 2941 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	1.0
DANN	Benign	0.32

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs5030789; hg19: chr15-40986355;