chr19-54491873-G-A

Variant names:

• chr19-54491873-G-A
• rs8111398

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 0.533 in 151,658 control chromosomes in the GnomAD database, including 22,339 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 0.53 (22339 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.599 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: 0.533 AC: 80789 AN: 151538 Hom.: 22336 Cov.: 30

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.533 AC: 80832 AN: 151658 Hom.: 22339 Cov.: 30 AF XY: 0.534 AC XY: 39599 AN XY: 74102

African (AFR) AF: 0.405 AC: 16711 AN: 41296

American (AMR) AF: 0.511 AC: 7778 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.606 AC: 2104 AN: 3472

East Asian (EAS) AF: 0.356 AC: 1838 AN: 5164

South Asian (SAS) AF: 0.599 AC: 2882 AN: 4810

European-Finnish (FIN) AF: 0.645 AC: 6762 AN: 10484

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.604 AC: 41022 AN: 67890

Other (OTH) AF: 0.530 AC: 1118 AN: 2108

Alfa AF: 0.573 Hom.: 25265

Bravo AF: 0.510

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.5
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs8111398; hg19: chr19-55003092;