rs1799281

Variant names:

• chr19-48445513-G-A
• rs1799281

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 0.65 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.530 AC: 21934 AN: 41394

American (AMR) AF: 0.699 AC: 10671 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2436 AN: 3468

East Asian (EAS) AF: 0.429 AC: 2213 AN: 5158

South Asian (SAS) AF: 0.496 AC: 2387 AN: 4816

European-Finnish (FIN) AF: 0.665 AC: 7025 AN: 10560

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.735 AC: 49931 AN: 67974

Other (OTH) AF: 0.636 AC: 1344 AN: 2114

Alfa AF: 0.696 Hom.: 26678

Bravo AF: 0.648

Asia WGS AF: 0.463 AC: 1611 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	15
DANN	Benign	0.86
PhyloP100		0.85
PromoterAI		-0.0056	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1799281; hg19: chr19-48948770;