rs559561

Variant names:

• chr15-49724099-A-G
• rs559561

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.253 AC: 10502 AN: 41502

American (AMR) AF: 0.492 AC: 7525 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 1608 AN: 3468

East Asian (EAS) AF: 0.494 AC: 2551 AN: 5166

South Asian (SAS) AF: 0.355 AC: 1713 AN: 4826

European-Finnish (FIN) AF: 0.518 AC: 5458 AN: 10530

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.438 AC: 29804 AN: 67972

Other (OTH) AF: 0.416 AC: 879 AN: 2114

Alfa AF: 0.430 Hom.: 57315

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
PhyloP100		3.0

Splicing

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

Other links and lift over

dbSNP: rs559561; hg19: chr15-50016296;