rs585451

Positions:

• chr15-49715528-A-G

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 0.327 in 152,082 control chromosomes in the GnomAD database, including 8,949 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 0.33 (8949 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.722

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49700 AN: 151964 Hom.: 8954 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.327 AC: 49720 AN: 152082 Hom.: 8949 Cov.: 32 AF XY: 0.329 AC XY: 24434 AN XY: 74336

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.413

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.470

Gnomad4 NFE AF: 0.393

Gnomad4 OTH AF: 0.352

Alfa AF: 0.375 Hom.: 11413

Bravo AF: 0.313

Asia WGS AF: 0.208 AC: 725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	14
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: rs585451; hg19: chr15-50007725;