rs1799281

Variant names:

• chr19-48445513-G-A
• rs1799281

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 0.65 in 151,950 control chromosomes in the GnomAD database, including 32,985 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 0.65 (32985 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.853

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.729 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: 0.650 AC: 98714 AN: 151830 Hom.: 32979 Cov.: 31

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.641

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

GnomAD4 genome AF: 0.650 AC: 98756 AN: 151950 Hom.: 32985 Cov.: 31 AF XY: 0.643 AC XY: 47741 AN XY: 74266

Gnomad4 AFR AF: 0.530

Gnomad4 AMR AF: 0.699

Gnomad4 ASJ AF: 0.702

Gnomad4 EAS AF: 0.429

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.665

Gnomad4 NFE AF: 0.735

Gnomad4 OTH AF: 0.636

Alfa AF: 0.703 Hom.: 19005

Bravo AF: 0.648

Asia WGS AF: 0.463 AC: 1611 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	15
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1799281; hg19: chr19-48948770;