8-115408099-A-T

Position:

• chr8-115408099-A-T

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 0.547 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.681

Gnomad4 AMR AF: 0.530

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.568

Gnomad4 SAS AF: 0.559

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.498

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs231150; hg19: chr8-116420327;