chr19-32873722-C-T

Variant names:

• chr19-32873722-C-T
• rs8101881

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 0.538 in 152,020 control chromosomes in the GnomAD database, including 22,814 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 0.54 (22814 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.431
• Publications: 42 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 (NFE) allele frequency at 95% confidence interval = 0.603 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: 0.539 AC: 81833 AN: 151902 Hom.: 22812 Cov.: 32

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.538 AC: 81857 AN: 152020 Hom.: 22814 Cov.: 32 AF XY: 0.541 AC XY: 40185 AN XY: 74308

African (AFR) AF: 0.413 AC: 17115 AN: 41476

American (AMR) AF: 0.573 AC: 8735 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1532 AN: 3472

East Asian (EAS) AF: 0.326 AC: 1686 AN: 5168

South Asian (SAS) AF: 0.543 AC: 2614 AN: 4814

European-Finnish (FIN) AF: 0.683 AC: 7205 AN: 10550

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.607 AC: 41289 AN: 67972

Other (OTH) AF: 0.511 AC: 1078 AN: 2110

Alfa AF: 0.576 Hom.: 119633

Bravo AF: 0.522

Asia WGS AF: 0.466 AC: 1618 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	8.7
DANN	Benign	0.78
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs8101881; hg19: chr19-33364628;