8-290578-T-A

Variant names:

• chr8-290578-T-A
• rs55680580

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 0.108 in 91,330 control chromosomes in the GnomAD database, including 482 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 0.11 (482 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.86
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.284 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: 0.108 AC: 9852 AN: 91262 Hom.: 484 Cov.: 26

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.0566

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.183

Gnomad NFE AF: 0.0889

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.108 AC: 9849 AN: 91330 Hom.: 482 Cov.: 26 AF XY: 0.111 AC XY: 5030 AN XY: 45224

African (AFR) AF: 0.109 AC: 2490 AN: 22940

American (AMR) AF: 0.0563 AC: 499 AN: 8856

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 249 AN: 2234

East Asian (EAS) AF: 0.299 AC: 1004 AN: 3358

South Asian (SAS) AF: 0.168 AC: 421 AN: 2504

European-Finnish (FIN) AF: 0.181 AC: 1112 AN: 6146

Middle Eastern (MID) AF: 0.144 AC: 17 AN: 118

European-Non Finnish (NFE) AF: 0.0889 AC: 3855 AN: 43382

Other (OTH) AF: 0.102 AC: 133 AN: 1304

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.56
DANN	Benign	0.20
PhyloP100		-3.9

Splicing

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

Other links and lift over

dbSNP: rs55680580; hg19: chr8-240578;