rs565819

Variant names:

• chr19-44463492-A-G
• rs565819

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 151,896 control chromosomes in the GnomAD database, including 8,392 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 (8392 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.679
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.407 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: 46382 AN: 151778 Hom.: 8394 Cov.: 31

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.305 AC: 46378 AN: 151896 Hom.: 8392 Cov.: 31 AF XY: 0.302 AC XY: 22448 AN XY: 74238

African (AFR) AF: 0.119 AC: 4910 AN: 41414

American (AMR) AF: 0.347 AC: 5303 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.357 AC: 1238 AN: 3470

East Asian (EAS) AF: 0.156 AC: 806 AN: 5182

South Asian (SAS) AF: 0.422 AC: 2029 AN: 4808

European-Finnish (FIN) AF: 0.300 AC: 3150 AN: 10516

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

European-Non Finnish (NFE) AF: 0.407 AC: 27617 AN: 67930

Other (OTH) AF: 0.338 AC: 711 AN: 2102

Alfa AF: 0.373 Hom.: 1927

Bravo AF: 0.298

Asia WGS AF: 0.268 AC: 932 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.75
DANN	Benign	0.46
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs565819; hg19: chr19-44967714;