rs1799281

chr19-48445513-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;