rs1808682

chr19-40983543-G-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 0.195 in 151,728 control chromosomes in the GnomAD database, including 3,471 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 0.19 (3471 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.251

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.257 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: 0.195 AC: 29536 AN: 151608 Hom.: 3470 Cov.: 31

Gnomad AFR AF: 0.0709

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.195 AC: 29536 AN: 151728 Hom.: 3471 Cov.: 31 AF XY: 0.195 AC XY: 14453 AN XY: 74098

Gnomad4 AFR AF: 0.0709

Gnomad4 AMR AF: 0.206

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.269

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.201

Alfa AF: 0.200 Hom.: 482

Bravo AF: 0.187

Asia WGS AF: 0.216 AC: 754 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.81
Dann	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1808682; hg19: chr19-41489448;