chr8-6939089-C-T

Variant names:

• chr8-6939089-C-T
• rs45482601

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 0.0777 in 152,164 control chromosomes in the GnomAD database, including 512 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 0.078 (512 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.709

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0777 AC: 11820 AN: 152046 Hom.: 512 Cov.: 32

Gnomad AFR AF: 0.0653

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.0834

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0695

Gnomad FIN AF: 0.0527

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0886

Gnomad OTH AF: 0.0939

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

GnomAD4 genome AF: 0.0777 AC: 11818 AN: 152164 Hom.: 512 Cov.: 32 AF XY: 0.0759 AC XY: 5648 AN XY: 74368

Gnomad4 AFR AF: 0.0651

Gnomad4 AMR AF: 0.0833

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0693

Gnomad4 FIN AF: 0.0527

Gnomad4 NFE AF: 0.0886

Gnomad4 OTH AF: 0.0929

Alfa AF: 0.0638 Hom.: 100

Bravo AF: 0.0795

Asia WGS AF: 0.0370 AC: 128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.9
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs45482601; hg19: chr8-6796611;