rs305009

Variant names:

• chr15-69853419-G-A
• rs305009

Variant summary

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

The variant allele was found at a frequency of 0.226 in 152,084 control chromosomes in the GnomAD database, including 3,948 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 0.23 (3948 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.757

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.299 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

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34316 AN: 151964 Hom.: 3945 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.226 AC: 34344 AN: 152084 Hom.: 3948 Cov.: 32 AF XY: 0.226 AC XY: 16799 AN XY: 74332

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.223

Alfa AF: 0.216 Hom.: 353

Bravo AF: 0.222

Asia WGS AF: 0.225 AC: 781 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.56
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs305009; hg19: chr15-70145758;