rs1822459

Variant names:

• chr18-50847757-T-C
• rs1822459

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 0.481 in 152,082 control chromosomes in the GnomAD database, including 20,520 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 0.48 (20520 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.878
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.68 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: 0.481 AC: 73126 AN: 151964 Hom.: 20513 Cov.: 33

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.481 AC: 73134 AN: 152082 Hom.: 20520 Cov.: 33 AF XY: 0.485 AC XY: 36057 AN XY: 74346

African (AFR) AF: 0.173 AC: 7171 AN: 41472

American (AMR) AF: 0.648 AC: 9904 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1972 AN: 3468

East Asian (EAS) AF: 0.449 AC: 2325 AN: 5180

South Asian (SAS) AF: 0.700 AC: 3380 AN: 4828

European-Finnish (FIN) AF: 0.580 AC: 6116 AN: 10552

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.593 AC: 40343 AN: 67984

Other (OTH) AF: 0.528 AC: 1116 AN: 2114

Alfa AF: 0.536 Hom.: 3928

Bravo AF: 0.471

Asia WGS AF: 0.572 AC: 1987 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.61
DANN	Benign	0.42
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs1822459; hg19: chr18-48374127;