15-40694157-A-G

Variant names:

• chr15-40694157-A-G
• rs5030789
• ENST00000499988.3:n.756T>C

Variant summary

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

The ENST00000499988.3(RAD51-AS1):​n.756T>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 ENST00000499988.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.99
• Publications: 17 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000499988.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RAD51-AS1	NR_040058.1		n.733T>C		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RAD51-AS1	ENST00000499988.3	TSL:2	n.756T>C		non_coding_transcript_exon	Exon 2 of 2
	RAD51-AS1	ENST00000671605.1		n.724T>C		non_coding_transcript_exon	Exon 2 of 2
	RAD51-AS1	ENST00000526635.2	TSL:2	n.300+429T>C		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 2 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.679 AC: 19 AN: 28

Other (OTH) AF: 1.00 AC: 2 AN: 2

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

African (AFR) AF: 0.691 AC: 28615 AN: 41432

American (AMR) AF: 0.686 AC: 10476 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.611 AC: 2116 AN: 3466

East Asian (EAS) AF: 0.926 AC: 4783 AN: 5164

South Asian (SAS) AF: 0.772 AC: 3720 AN: 4818

European-Finnish (FIN) AF: 0.693 AC: 7310 AN: 10544

Middle Eastern (MID) AF: 0.652 AC: 189 AN: 290

European-Non Finnish (NFE) AF: 0.579 AC: 39335 AN: 67942

Other (OTH) AF: 0.624 AC: 1308 AN: 2096

Alfa AF: 0.525 Hom.: 1626

Bravo AF: 0.651

Asia WGS AF: 0.846 AC: 2941 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.32
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs5030789; hg19: chr15-40986355;