rs5022079

Variant names:

• chr18-78718188-A-G
• rs5022079

Your query was ambiguous. Multiple possible variants found:

• chr18-78718188-A-G
• chr18-78718188-A-T

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 0.74 in 152,204 control chromosomes in the GnomAD database, including 43,210 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 0.74 (43210 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.841 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: 0.740 AC: 112596 AN: 152086 Hom.: 43217 Cov.: 34

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.866

Gnomad EAS AF: 0.798

Gnomad SAS AF: 0.830

Gnomad FIN AF: 0.828

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.847

Gnomad OTH AF: 0.755

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

GnomAD4 genome AF: 0.740 AC: 112612 AN: 152204 Hom.: 43210 Cov.: 34 AF XY: 0.742 AC XY: 55200 AN XY: 74388

African (AFR) AF: 0.524 AC: 21752 AN: 41506

American (AMR) AF: 0.703 AC: 10751 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.866 AC: 3006 AN: 3472

East Asian (EAS) AF: 0.797 AC: 4108 AN: 5152

South Asian (SAS) AF: 0.829 AC: 4003 AN: 4826

European-Finnish (FIN) AF: 0.828 AC: 8778 AN: 10606

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.847 AC: 57628 AN: 68024

Other (OTH) AF: 0.753 AC: 1591 AN: 2112

Alfa AF: 0.766 Hom.: 7984

Bravo AF: 0.720

Asia WGS AF: 0.782 AC: 2716 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.66
DANN	Benign	0.38
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs5022079; hg19: chr18-76478188;