19-40983543-G-A

Variant names:

• chr19-40983543-G-A
• rs1808682

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 0.195 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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.0709 AC: 2926 AN: 41298

American (AMR) AF: 0.206 AC: 3142 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 829 AN: 3472

East Asian (EAS) AF: 0.269 AC: 1385 AN: 5156

South Asian (SAS) AF: 0.211 AC: 1014 AN: 4802

European-Finnish (FIN) AF: 0.257 AC: 2695 AN: 10492

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.247 AC: 16767 AN: 67948

Other (OTH) AF: 0.201 AC: 423 AN: 2106

Alfa AF: 0.208 Hom.: 1107

Bravo AF: 0.187

Asia WGS AF: 0.216 AC: 754 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.81
DANN	Benign	0.88
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs1808682; hg19: chr19-41489448;