rs565819

Positions:

• chr19-44463492-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.357

Gnomad4 EAS AF: 0.156

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.300

Gnomad4 NFE AF: 0.407

Gnomad4 OTH AF: 0.338

Alfa AF: 0.380 Hom.: 1921

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs565819; hg19: chr19-44967714;