chr8-21905882-A-G

Variant names:

• chr8-21905882-A-G
• rs1479056

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 0.564 in 152,046 control chromosomes in the GnomAD database, including 25,203 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 0.56 (25203 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.20
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.789 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: 0.564 AC: 85725 AN: 151928 Hom.: 25182 Cov.: 33

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.727

Gnomad AMR AF: 0.687

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.564 AC: 85796 AN: 152046 Hom.: 25203 Cov.: 33 AF XY: 0.575 AC XY: 42723 AN XY: 74318

African (AFR) AF: 0.409 AC: 16942 AN: 41470

American (AMR) AF: 0.688 AC: 10505 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 2090 AN: 3466

East Asian (EAS) AF: 0.809 AC: 4186 AN: 5174

South Asian (SAS) AF: 0.670 AC: 3226 AN: 4818

European-Finnish (FIN) AF: 0.672 AC: 7094 AN: 10564

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.583 AC: 39640 AN: 67960

Other (OTH) AF: 0.600 AC: 1267 AN: 2110

Alfa AF: 0.553 Hom.: 8679

Bravo AF: 0.561

Asia WGS AF: 0.698 AC: 2426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.058
DANN	Benign	0.25
PhyloP100		-4.2

Splicing

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

Other links and lift over

dbSNP: rs1479056; hg19: chr8-21763393;