8-9928984-A-G

Position:

• chr8-9928984-A-G

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 0.878 in 152,282 control chromosomes in the GnomAD database, including 58,813 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 0.88 (58813 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.128

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.902 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: 0.878 AC: 133673 AN: 152164 Hom.: 58777 Cov.: 33

Gnomad AFR AF: 0.910

Gnomad AMI AF: 0.894

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.920

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.883

Gnomad FIN AF: 0.806

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.876

Gnomad OTH AF: 0.883

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

GnomAD4 genome AF: 0.878 AC: 133765 AN: 152282 Hom.: 58813 Cov.: 33 AF XY: 0.876 AC XY: 65240 AN XY: 74454

Gnomad4 AFR AF: 0.910

Gnomad4 AMR AF: 0.860

Gnomad4 ASJ AF: 0.920

Gnomad4 EAS AF: 0.827

Gnomad4 SAS AF: 0.883

Gnomad4 FIN AF: 0.806

Gnomad4 NFE AF: 0.876

Gnomad4 OTH AF: 0.877

Alfa AF: 0.878 Hom.: 77180

Bravo AF: 0.880

Asia WGS AF: 0.833 AC: 2897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.1
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs586123; hg19: chr8-9786494;