rs559561

Positions:

• chr15-49724099-A-G

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4 BA1

The variant allele was found at a frequency of 0.398 in 152,066 control chromosomes in the GnomAD database, including 12,793 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 0.40 (12793 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.04

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.13).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60434 AN: 151946 Hom.: 12788 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.398 AC: 60450 AN: 152066 Hom.: 12793 Cov.: 32 AF XY: 0.404 AC XY: 30025 AN XY: 74326

Gnomad4 AFR AF: 0.253

Gnomad4 AMR AF: 0.492

Gnomad4 ASJ AF: 0.464

Gnomad4 EAS AF: 0.494

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.518

Gnomad4 NFE AF: 0.438

Gnomad4 OTH AF: 0.416

Alfa AF: 0.435 Hom.: 24710

Bravo AF: 0.395

Asia WGS AF: 0.385 AC: 1343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.13
CADD	Benign	21
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs559561; hg19: chr15-50016296;