8-115408099-A-T

Variant names:

• chr8-115408099-A-T
• rs231150

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 0.547 in 151,218 control chromosomes in the GnomAD database, including 23,330 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 0.55 (23330 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.95
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.674 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: 0.547 AC: 82624 AN: 151100 Hom.: 23309 Cov.: 29

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.567

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.547 AC: 82693 AN: 151218 Hom.: 23330 Cov.: 29 AF XY: 0.544 AC XY: 40133 AN XY: 73838

African (AFR) AF: 0.681 AC: 28109 AN: 41278

American (AMR) AF: 0.530 AC: 8014 AN: 15128

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 1372 AN: 3456

East Asian (EAS) AF: 0.568 AC: 2871 AN: 5056

South Asian (SAS) AF: 0.559 AC: 2691 AN: 4818

European-Finnish (FIN) AF: 0.408 AC: 4264 AN: 10440

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33688 AN: 67736

Other (OTH) AF: 0.498 AC: 1048 AN: 2104

Alfa AF: 0.524 Hom.: 2787

Bravo AF: 0.561

Asia WGS AF: 0.541 AC: 1864 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	10
DANN	Benign	0.64
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs231150; hg19: chr8-116420327;