rs798887

Variant names:

• chr19-54289334-G-A
• rs798887

Your query was ambiguous. Multiple possible variants found:

• chr19-54289334-G-A
• chr19-54289334-G-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	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

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.500

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

Gnomad4 AFR AF: 0.815

Gnomad4 AMR AF: 0.618

Gnomad4 ASJ AF: 0.910

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.817

Gnomad4 FIN AF: 0.677

Gnomad4 NFE AF: 0.790

Gnomad4 OTH AF: 0.788

Alfa AF: 0.819 Hom.: 33008

Bravo AF: 0.750

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs798887; hg19: chr19-54793188;