rs1682809

Variant names:

• chr19-3165897-G-A
• rs1682809

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 0.437 in 151,982 control chromosomes in the GnomAD database, including 14,894 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 0.44 (14894 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.670

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.489 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: 0.437 AC: 66425 AN: 151864 Hom.: 14889 Cov.: 32

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.437 AC: 66452 AN: 151982 Hom.: 14894 Cov.: 32 AF XY: 0.432 AC XY: 32115 AN XY: 74272

Gnomad4 AFR AF: 0.370

Gnomad4 AMR AF: 0.399

Gnomad4 ASJ AF: 0.513

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.454

Gnomad4 NFE AF: 0.493

Gnomad4 OTH AF: 0.451

Alfa AF: 0.482 Hom.: 35843

Bravo AF: 0.434

Asia WGS AF: 0.327 AC: 1138 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	1.3
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1682809; hg19: chr19-3165895;