chr19-33326227-A-G

Variant names:

• chr19-33326227-A-G
• rs12608723

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 0.23 in 151,930 control chromosomes in the GnomAD database, including 5,174 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 0.23 (5174 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.41 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: 0.229 AC: 34834 AN: 151810 Hom.: 5153 Cov.: 31

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.188

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.230 AC: 34894 AN: 151930 Hom.: 5174 Cov.: 31 AF XY: 0.230 AC XY: 17097 AN XY: 74240

African (AFR) AF: 0.415 AC: 17170 AN: 41386

American (AMR) AF: 0.253 AC: 3856 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 413 AN: 3466

East Asian (EAS) AF: 0.192 AC: 987 AN: 5152

South Asian (SAS) AF: 0.228 AC: 1092 AN: 4798

European-Finnish (FIN) AF: 0.168 AC: 1775 AN: 10562

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 8986 AN: 67992

Other (OTH) AF: 0.210 AC: 444 AN: 2112

Alfa AF: 0.156 Hom.: 1970

Bravo AF: 0.246

Asia WGS AF: 0.199 AC: 696 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.1
DANN	Benign	0.49
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs12608723; hg19: chr19-33817133;