rs1683564

chr19-859214-C-A

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 0.314 in 152,070 control chromosomes in the GnomAD database, including 7,987 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 (7987 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.673

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47801 AN: 151952 Hom.: 7988 Cov.: 33

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.314 AC: 47798 AN: 152070 Hom.: 7987 Cov.: 33 AF XY: 0.318 AC XY: 23674 AN XY: 74342

Gnomad4 AFR AF: 0.189

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.364

Gnomad4 EAS AF: 0.295

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.315

Alfa AF: 0.348 Hom.: 11332

Bravo AF: 0.311

Asia WGS AF: 0.359 AC: 1253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.5
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1683564; hg19: chr19-859214;