chr19-54289334-G-A

Variant names:

• chr19-54289334-G-A
• rs798887

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 0.76 in 149,610 control chromosomes in the GnomAD database, including 44,296 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 0.76 (44296 hom., cov: 25)
  • Exomes 𝑓: 0.25 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.09).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.808 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: 0.760 AC: 113690 AN: 149498 Hom.: 44266 Cov.: 25

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.889

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.817

Gnomad FIN AF: 0.677

Gnomad MID AF: 0.895

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.788

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.250 AC: 2 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.250 AC XY: 1 AN XY: 4

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 2 AN: 4

Other (OTH) AC: 0 AN: 0

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.00233887), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.760 AC: 113768 AN: 149610 Hom.: 44296 Cov.: 25 AF XY: 0.752 AC XY: 54858 AN XY: 72940

African (AFR) AF: 0.815 AC: 33163 AN: 40684

American (AMR) AF: 0.618 AC: 9241 AN: 14954

Ashkenazi Jewish (ASJ) AF: 0.910 AC: 3119 AN: 3428

East Asian (EAS) AF: 0.328 AC: 1686 AN: 5136

South Asian (SAS) AF: 0.817 AC: 3829 AN: 4684

European-Finnish (FIN) AF: 0.677 AC: 6936 AN: 10246

Middle Eastern (MID) AF: 0.894 AC: 261 AN: 292

European-Non Finnish (NFE) AF: 0.790 AC: 53103 AN: 67218

Other (OTH) AF: 0.788 AC: 1623 AN: 2060

Alfa AF: 0.798 Hom.: 66427

Bravo AF: 0.750

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.17
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs798887; hg19: chr19-54793188;