chr8-27459526-T-C

Position:

• chr8-27459526-T-C

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 0.855 in 205,416 control chromosomes in the GnomAD database, including 75,877 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 0.86 (57039 hom., cov: 33)
  • Exomes 𝑓: 0.83 (18838 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07

Genes affected

(HGNC:):

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 = 0.89 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.27459526T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.863 AC: 131189 AN: 152068 Hom.: 56991 Cov.: 33

Gnomad AFR AF: 0.898

Gnomad AMI AF: 0.913

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.939

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.848

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.874

Gnomad OTH AF: 0.882

GnomAD4 exome AF: 0.832 AC: 44291 AN: 53228 Hom.: 18838 AF XY: 0.837 AC XY: 20794 AN XY: 24850

Gnomad4 AFR exome AF: 0.908

Gnomad4 AMR exome AF: 0.840

Gnomad4 ASJ exome AF: 0.929

Gnomad4 EAS exome AF: 0.567

Gnomad4 SAS exome AF: 0.859

Gnomad4 FIN exome AF: 0.947

Gnomad4 NFE exome AF: 0.876

Gnomad4 OTH exome AF: 0.876

GnomAD4 genome AF: 0.863 AC: 131291 AN: 152188 Hom.: 57039 Cov.: 33 AF XY: 0.857 AC XY: 63788 AN XY: 74400

Gnomad4 AFR AF: 0.898

Gnomad4 AMR AF: 0.827

Gnomad4 ASJ AF: 0.939

Gnomad4 EAS AF: 0.534

Gnomad4 SAS AF: 0.846

Gnomad4 FIN AF: 0.837

Gnomad4 NFE AF: 0.874

Gnomad4 OTH AF: 0.883

Alfa AF: 0.870 Hom.: 9745

Bravo AF: 0.865

Asia WGS AF: 0.736 AC: 2559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.048
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs748281; hg19: chr8-27317043;