8-80624879-G-A

Variant names:

• chr8-80624879-G-A
• rs7000234

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 0.0992 in 152,124 control chromosomes in the GnomAD database, including 1,082 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 0.099 (1082 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730
• Publications: 3 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 (AFR) allele frequency at 95% confidence interval = 0.196 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: 0.0989 AC: 15037 AN: 152006 Hom.: 1069 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.0648

Gnomad AMR AF: 0.0648

Gnomad ASJ AF: 0.0799

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0172

Gnomad FIN AF: 0.0611

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0664

Gnomad OTH AF: 0.0982

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

GnomAD4 genome AF: 0.0992 AC: 15084 AN: 152124 Hom.: 1082 Cov.: 32 AF XY: 0.0967 AC XY: 7193 AN XY: 74380

African (AFR) AF: 0.200 AC: 8279 AN: 41480

American (AMR) AF: 0.0645 AC: 986 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0799 AC: 277 AN: 3468

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5188

South Asian (SAS) AF: 0.0175 AC: 84 AN: 4810

European-Finnish (FIN) AF: 0.0611 AC: 647 AN: 10590

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0663 AC: 4510 AN: 67980

Other (OTH) AF: 0.0976 AC: 206 AN: 2110

Alfa AF: 0.0721 Hom.: 274

Bravo AF: 0.103

Asia WGS AF: 0.0230 AC: 81 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	5.1
DANN	Benign	0.82
PhyloP100		0.073

Splicing

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

Other links and lift over

dbSNP: rs7000234; hg19: chr8-81537114;