chr8-54356925-G-T

Position:

• chr8-54356925-G-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 0.0806 in 152,124 control chromosomes in the GnomAD database, including 633 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 0.081 (633 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.625

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.54356925G>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0806 AC: 12246 AN: 152010 Hom.: 631 Cov.: 33

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.0606

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.0410

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.0313

Gnomad FIN AF: 0.0977

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0456

Gnomad OTH AF: 0.0742

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

GnomAD4 genome AF: 0.0806 AC: 12263 AN: 152124 Hom.: 633 Cov.: 33 AF XY: 0.0828 AC XY: 6159 AN XY: 74352

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.0410

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.0309

Gnomad4 FIN AF: 0.0977

Gnomad4 NFE AF: 0.0456

Gnomad4 OTH AF: 0.0734

Alfa AF: 0.0532 Hom.: 631

Bravo AF: 0.0865

Asia WGS AF: 0.0890 AC: 310 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.55
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: rs7827900; hg19: chr8-55269485;