rs5030783

Variant names:

• chr15-40692191-T-C
• rs5030783
• ENST00000526635.2:n.300+2395A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000526635.2(RAD51-AS1):​n.300+2395A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 152,098 control chromosomes in the GnomAD database, including 6,453 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 0.27 (6453 hom., cov: 31)
• Consequence: RAD51-AS1 ENST00000526635.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.442
• Publications: 12 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAD51-AS1	ENST00000526635.2	n.300+2395A>G		intron_variant	Intron 2 of 2	2
RAD51-AS1	ENST00000533146.5	n.295+2395A>G		intron_variant	Intron 2 of 2	3
RAD51-AS1	ENST00000650326.1	n.292+2395A>G		intron_variant	Intron 2 of 3
RAD51-AS1	ENST00000743886.1	n.120+2581A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40673 AN: 151980 Hom.: 6451 Cov.: 31

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.267 AC: 40677 AN: 152098 Hom.: 6453 Cov.: 31 AF XY: 0.272 AC XY: 20233 AN XY: 74348

African (AFR) AF: 0.113 AC: 4692 AN: 41510

American (AMR) AF: 0.250 AC: 3816 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1243 AN: 3470

East Asian (EAS) AF: 0.101 AC: 521 AN: 5182

South Asian (SAS) AF: 0.343 AC: 1650 AN: 4814

European-Finnish (FIN) AF: 0.430 AC: 4548 AN: 10568

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.343 AC: 23319 AN: 67962

Other (OTH) AF: 0.265 AC: 560 AN: 2114

Alfa AF: 0.297 Hom.: 1146

Bravo AF: 0.242

Asia WGS AF: 0.248 AC: 862 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	1.6
DANN	Benign	0.94
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs5030783; hg19: chr15-40984389;