rs566514

Variant names:

• chr13-33079202-T-C
• rs566514

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 0.305 in 152,130 control chromosomes in the GnomAD database, including 8,541 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 0.31 (8541 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720
• Publications: 3 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 (AMR) 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: 0.306 AC: 46442 AN: 152012 Hom.: 8526 Cov.: 31

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.305 AC: 46472 AN: 152130 Hom.: 8541 Cov.: 31 AF XY: 0.309 AC XY: 22953 AN XY: 74358

African (AFR) AF: 0.111 AC: 4626 AN: 41526

American (AMR) AF: 0.493 AC: 7535 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1401 AN: 3468

East Asian (EAS) AF: 0.251 AC: 1293 AN: 5156

South Asian (SAS) AF: 0.298 AC: 1438 AN: 4822

European-Finnish (FIN) AF: 0.394 AC: 4162 AN: 10572

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.365 AC: 24819 AN: 67980

Other (OTH) AF: 0.341 AC: 719 AN: 2110

Alfa AF: 0.340 Hom.: 1666

Bravo AF: 0.310

Asia WGS AF: 0.312 AC: 1088 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	1.6
DANN	Benign	0.51
PhyloP100		-0.072

Splicing

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

Other links and lift over

dbSNP: rs566514; hg19: chr13-33653339;