chr8-59177738-A-G

Variant names:

• chr8-59177738-A-G
• rs10086929

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 0.46 in 151,544 control chromosomes in the GnomAD database, including 16,520 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 0.46 (16520 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.424
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.459 AC: 69579 AN: 151424 Hom.: 16504 Cov.: 30

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.460 AC: 69635 AN: 151544 Hom.: 16520 Cov.: 30 AF XY: 0.452 AC XY: 33453 AN XY: 74028

African (AFR) AF: 0.472 AC: 19471 AN: 41230

American (AMR) AF: 0.576 AC: 8769 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1575 AN: 3470

East Asian (EAS) AF: 0.546 AC: 2817 AN: 5162

South Asian (SAS) AF: 0.299 AC: 1432 AN: 4792

European-Finnish (FIN) AF: 0.291 AC: 3037 AN: 10438

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30670 AN: 67900

Other (OTH) AF: 0.506 AC: 1068 AN: 2110

Alfa AF: 0.443 Hom.: 1894

Bravo AF: 0.490

Asia WGS AF: 0.418 AC: 1455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.71
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs10086929; hg19: chr8-60090297;