rs2569530

Variant names:

• chr19-50905352-C-A
• rs2569530

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.404 in 152,074 control chromosomes in the GnomAD database, including 13,456 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 (13456 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.566
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.477 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: 0.404 AC: 61441 AN: 151956 Hom.: 13455 Cov.: 31

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.0508

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.404 AC: 61474 AN: 152074 Hom.: 13456 Cov.: 31 AF XY: 0.404 AC XY: 30047 AN XY: 74328

African (AFR) AF: 0.274 AC: 11360 AN: 41478

American (AMR) AF: 0.453 AC: 6918 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1799 AN: 3468

East Asian (EAS) AF: 0.0513 AC: 266 AN: 5182

South Asian (SAS) AF: 0.317 AC: 1526 AN: 4810

European-Finnish (FIN) AF: 0.509 AC: 5370 AN: 10558

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.482 AC: 32733 AN: 67980

Other (OTH) AF: 0.422 AC: 891 AN: 2110

Alfa AF: 0.445 Hom.: 2000

Bravo AF: 0.394

Asia WGS AF: 0.190 AC: 664 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	6.0
DANN	Benign	0.57
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs2569530; hg19: chr19-51408608;