19-33831232-A-G

Variant names:

• chr19-33831232-A-G
• rs11084753

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 0.644 in 151,984 control chromosomes in the GnomAD database, including 31,790 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 0.64 (31790 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.82
• Publications: 107 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.668 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: 0.644 AC: 97790 AN: 151866 Hom.: 31778 Cov.: 32

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.644 AC: 97847 AN: 151984 Hom.: 31790 Cov.: 32 AF XY: 0.641 AC XY: 47632 AN XY: 74284

African (AFR) AF: 0.639 AC: 26485 AN: 41462

American (AMR) AF: 0.652 AC: 9951 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.621 AC: 2155 AN: 3470

East Asian (EAS) AF: 0.331 AC: 1705 AN: 5152

South Asian (SAS) AF: 0.580 AC: 2794 AN: 4816

European-Finnish (FIN) AF: 0.663 AC: 6993 AN: 10546

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.673 AC: 45738 AN: 67962

Other (OTH) AF: 0.624 AC: 1317 AN: 2110

Alfa AF: 0.655 Hom.: 110436

Bravo AF: 0.643

Asia WGS AF: 0.482 AC: 1680 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.063
DANN	Benign	0.075
PhyloP100		-3.8

Splicing

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

Other links and lift over

dbSNP: rs11084753; hg19: chr19-34322137;