chr8-28228571-G-A

Position:

• chr8-28228571-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.672 in 152,022 control chromosomes in the GnomAD database, including 34,882 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 0.67 (34882 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.167

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.844 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.672 AC: 102055 AN: 151904 Hom.: 34870 Cov.: 32

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.800

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.727

Gnomad OTH AF: 0.683

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

GnomAD4 genome AF: 0.672 AC: 102111 AN: 152022 Hom.: 34882 Cov.: 32 AF XY: 0.670 AC XY: 49772 AN XY: 74296

Gnomad4 AFR AF: 0.559

Gnomad4 AMR AF: 0.608

Gnomad4 ASJ AF: 0.800

Gnomad4 EAS AF: 0.865

Gnomad4 SAS AF: 0.770

Gnomad4 FIN AF: 0.666

Gnomad4 NFE AF: 0.727

Gnomad4 OTH AF: 0.683

Alfa AF: 0.674 Hom.: 5510

Bravo AF: 0.663

Asia WGS AF: 0.776 AC: 2698 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.6
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6985069; hg19: chr8-28086088;