8-28491521-G-A

Variant names:

• chr8-28491521-G-A
• rs3757888

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 0.833 in 152,106 control chromosomes in the GnomAD database, including 53,271 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 0.83 (53271 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.736
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.905 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: 0.833 AC: 126584 AN: 151988 Hom.: 53243 Cov.: 33

Gnomad AFR AF: 0.717

Gnomad AMI AF: 0.950

Gnomad AMR AF: 0.889

Gnomad ASJ AF: 0.906

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.928

Gnomad FIN AF: 0.883

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.866

Gnomad OTH AF: 0.845

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

GnomAD4 genome AF: 0.833 AC: 126663 AN: 152106 Hom.: 53271 Cov.: 33 AF XY: 0.836 AC XY: 62146 AN XY: 74342

African (AFR) AF: 0.716 AC: 29694 AN: 41454

American (AMR) AF: 0.889 AC: 13599 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.906 AC: 3143 AN: 3470

East Asian (EAS) AF: 0.891 AC: 4624 AN: 5190

South Asian (SAS) AF: 0.928 AC: 4475 AN: 4822

European-Finnish (FIN) AF: 0.883 AC: 9323 AN: 10562

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.866 AC: 58884 AN: 68000

Other (OTH) AF: 0.847 AC: 1788 AN: 2112

Alfa AF: 0.852 Hom.: 6889

Bravo AF: 0.828

Asia WGS AF: 0.910 AC: 3163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.4
DANN	Benign	0.71
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs3757888; hg19: chr8-28349038;