chr19-45664843-A-G

Variant names:

• chr19-45664843-A-G
• rs8111428

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 0.244 in 151,832 control chromosomes in the GnomAD database, including 4,999 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 0.24 (4999 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.696
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.244 AC: 36987 AN: 151714 Hom.: 4998 Cov.: 30

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.0768

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.244 AC: 37017 AN: 151832 Hom.: 4999 Cov.: 30 AF XY: 0.242 AC XY: 17953 AN XY: 74198

African (AFR) AF: 0.370 AC: 15268 AN: 41320

American (AMR) AF: 0.241 AC: 3677 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 975 AN: 3470

East Asian (EAS) AF: 0.0768 AC: 397 AN: 5170

South Asian (SAS) AF: 0.237 AC: 1139 AN: 4816

European-Finnish (FIN) AF: 0.189 AC: 1998 AN: 10554

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.189 AC: 12846 AN: 67960

Other (OTH) AF: 0.224 AC: 471 AN: 2106

Alfa AF: 0.218 Hom.: 1722

Bravo AF: 0.252

Asia WGS AF: 0.183 AC: 634 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.9
DANN	Benign	0.33
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs8111428; hg19: chr19-46168101; COSMIC: COSV54424869;