rs5030783

Positions:

• chr15-40692191-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.442

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.40692191T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RAD51-AS1	ENST00000526635.2	n.300+2395A>G		intron_variant		2
RAD51-AS1	ENST00000533146.5	n.295+2395A>G		intron_variant		3
RAD51-AS1	ENST00000650326.1	n.292+2395A>G		intron_variant

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

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.343

Gnomad4 FIN AF: 0.430

Gnomad4 NFE AF: 0.343

Gnomad4 OTH AF: 0.265

Alfa AF: 0.304 Hom.: 1143

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5030783; hg19: chr15-40984389;