8-21558693-A-G

Variant names:

• chr8-21558693-A-G
• rs7836489

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 0.441 in 152,016 control chromosomes in the GnomAD database, including 15,171 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 0.44 (15171 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490
• Publications: 2 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 = 0.52 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.441 AC: 66980 AN: 151898 Hom.: 15135 Cov.: 32

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.441 AC: 67072 AN: 152016 Hom.: 15171 Cov.: 32 AF XY: 0.443 AC XY: 32931 AN XY: 74332

African (AFR) AF: 0.525 AC: 21777 AN: 41442

American (AMR) AF: 0.390 AC: 5956 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.445 AC: 1544 AN: 3470

East Asian (EAS) AF: 0.435 AC: 2239 AN: 5152

South Asian (SAS) AF: 0.532 AC: 2560 AN: 4812

European-Finnish (FIN) AF: 0.441 AC: 4663 AN: 10580

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.396 AC: 26929 AN: 67952

Other (OTH) AF: 0.410 AC: 865 AN: 2112

Alfa AF: 0.401 Hom.: 13791

Bravo AF: 0.439

Asia WGS AF: 0.511 AC: 1778 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.46
DANN	Benign	0.88
PhyloP100		-0.049

Splicing

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

Other links and lift over

dbSNP: rs7836489; hg19: chr8-21416204;