19-47213090-T-A

Variant names:

• chr19-47213090-T-A
• rs884171

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 0.784 in 152,016 control chromosomes in the GnomAD database, including 47,399 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 0.78 (47399 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.279
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.783 AC: 119002 AN: 151900 Hom.: 47348 Cov.: 32

Gnomad AFR AF: 0.923

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.764

Gnomad EAS AF: 0.942

Gnomad SAS AF: 0.917

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.777

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

GnomAD4 genome AF: 0.784 AC: 119111 AN: 152016 Hom.: 47399 Cov.: 32 AF XY: 0.786 AC XY: 58408 AN XY: 74296

African (AFR) AF: 0.923 AC: 38228 AN: 41426

American (AMR) AF: 0.723 AC: 11021 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.764 AC: 2652 AN: 3470

East Asian (EAS) AF: 0.942 AC: 4889 AN: 5190

South Asian (SAS) AF: 0.917 AC: 4428 AN: 4828

European-Finnish (FIN) AF: 0.721 AC: 7619 AN: 10570

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.703 AC: 47813 AN: 67976

Other (OTH) AF: 0.779 AC: 1641 AN: 2106

Alfa AF: 0.748 Hom.: 5355

Bravo AF: 0.789

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.56
DANN	Benign	0.71
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs884171; hg19: chr19-47716347;