rs790314

Variant names:

• chr18-28832668-A-G
• rs790314

Your query was ambiguous. Multiple possible variants found:

• chr18-28832668-A-G
• chr18-28832668-A-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.587 in 152,012 control chromosomes in the GnomAD database, including 27,113 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 0.59 (27113 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.746 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.586 AC: 89078 AN: 151892 Hom.: 27075 Cov.: 33

Gnomad AFR AF: 0.738

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.767

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.587 AC: 89172 AN: 152012 Hom.: 27113 Cov.: 33 AF XY: 0.589 AC XY: 43761 AN XY: 74270

African (AFR) AF: 0.738 AC: 30628 AN: 41504

American (AMR) AF: 0.583 AC: 8907 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1479 AN: 3464

East Asian (EAS) AF: 0.766 AC: 3952 AN: 5160

South Asian (SAS) AF: 0.601 AC: 2896 AN: 4822

European-Finnish (FIN) AF: 0.532 AC: 5607 AN: 10538

Middle Eastern (MID) AF: 0.486 AC: 142 AN: 292

European-Non Finnish (NFE) AF: 0.500 AC: 33998 AN: 67952

Other (OTH) AF: 0.528 AC: 1115 AN: 2110

Alfa AF: 0.550 Hom.: 2938

Bravo AF: 0.594

Asia WGS AF: 0.666 AC: 2313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	13
DANN	Benign	0.76
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs790314; hg19: chr18-26412633;